The first stage contained no major difficulties, with the only categorised climb of the 164 km (101.9 mi) parcours being a Category 3 climb, the Alto Saladillo, situated 55 km (34 mi) from the start. From that point, the course was mostly a descending false flat to the finish in Villa Mercedes.
A breakaway of seven riders racing for non-World Tour teams formed and enjoyed a lead of eight minutes as they crested the Alto Saladillo. Flavio de Luna from a Mexican selective team was the first atop the climb, which earned him the red jersey for the mountains classification leader at the end of the stage. Upon the descent, the sprinters' teams Omega Pharma-Quick Step, Cannondale, Androni Giocattoli-Venezuela and Lampre-Merida took station at the front of the peloton, bringing the escapees' advantage down to four minutes with 55 km (34 mi) remaining. The remnants of the break were ultimately caught in the closing stages, setting up a bunch sprint finish.Peter Sagan tried to lead-out his teammate Lucas Sebastián Haedo to the line, but a crash occurred in the final 500 metres (1,600 feet) stunting most teams' lead-outs. Mark Cavendish avoided the incident, launching from the Lampre-Merida train and won clearly, ahead of rivals Sacha Modolo and Alessandro Petacchi, to take a début victory for his new team, Omega Pharma-Quick Step.
The parcours for the second stage was relatively similar to the previous stage, with only one categorised climb – the third-category Alto Paso Grande coming in the first third of the race – during its 171.4 km (106.5 mi) itinerary. The finish at Terrazas del Portezuelo provided the riders with a twisty uphill finish, but was still expected to provide a sprint finish.
A five-rider move went clear after 8 km (5.0 mi) of racing, including Emmanuel Guevara of local team San Luis Somos Todos, who was first atop the only climb of the day, moving him level on points with the mountains classification leader, Flavio de Luna. Guevara later had to depart from the breakaway due to him feeling unwell. Nevertheless, the break enjoyed a maximum lead of almost five minutes, but was reeled in mostly by the Cannondale and Omega Pharma-Quick Step teams. Sacha Modolo of Bardiani Valvole-CSF Inox derailed the big teams plans as he beat rivals Mark Cavendish and Leigh Howard in the sprint. Modolo confided afterward that he learned the finish was uphill during the race while chatting with other riders, as he first thought it would be flat. Along with the victory, Modolo assumed the leader's jersey from Cavendish, on countback.
Stage 3 was denoted as the queen stage of the race, and included two categorised climbs in the opening half of the stage; a third-category climb was followed by the first-category Alto de Nogoli climb, at the midway point. The stage continued up to a summit finish, on the first-category Mirador del Potrero, above Lake Potrero de los Funes.
A breakaway of seven riders went clear early on, and included San Luis Somos Todos teammates Jorge Giacinti and Leandro Messineo. Giacinti was the first rider to cross each of the first two climbs of the day in front, collecting enough points to take the mountains classification jersey. Messineo would also join Giacinti during the post-stage ceremonies, as he won the two intermediate sprints of the stage, which was sufficient to take the sprint classification jersey from Walter Pérez. The breakaway was eventually caught by a group of forty riders with 30 kilometres (19 mi) to go.
The individual time trial stage was mainly flat, with an elevation change of 100 metres (330 ft) over the first 10 kilometres (6.2 mi), at which point the riders took a 180-degree hairpin turn and rode the course in the opposite direction, back to the starting point.
The first 130 kilometres (81 mi) of Stage 5 were mostly flat, before two categorised climbs within the final 40 kilometres (25 mi). A third-category climb was immediately followed by the first-category Cerro al Amago ascent, a climb of 10.5 kilometres (6.5 mi) in length with an average gradient of 7.2%. The terrain then became mostly flat until the finish line in Carolina.
Emmanuel Guevara of San Luis Somos Todos and Vojtěch Hačecký of ASC Dukla Praha broke away early and were given some freedom by the peloton since neither rider was a threat for the overall classification. Enjoying the tailwind, the duo had a maximum gap of seventeen minutes. Guevara dropped Hačecký on the slopes of the Cerro al Amago, and still had an advantage of fifteen minutes with 24 kilometres (15 mi) to go. The bunch tackled with the climb and BMC Racing Team put the pressure on, working for their leader Tejay van Garderen, who had been in second place in the general classification overnight, 23 seconds behind the leader Michał Kwiatkowski of Omega Pharma-Quick Step. Kwiatkowski himself was struggling on the climb, and was soon distanced, and ensured that the leader's jersey would change hands again. Alberto Contador and Daniel Díaz attacked, but Contador could not sustain the tempo set by Díaz, and fell back to the small group containing van Garderen. Díaz almost made the junction with his fading teammate Guevara, finishing fifteen seconds behind. Guevara barely had the strength for a victory salute, as he crossed the line by swerving dangerously. The stage was a double success for their San Luis Somos Todos team, since Díaz had gained enough time to move in the first spot of the general classification.
26 January 2013 — Quines to Merlo–Mirador del Sol, 156.6 km (97.3 mi)
Stage 6 was the last mountain stage of the Tour. It contained three categorised climbs, starting with the second-category Alto de Cantana in the first half of the race. The course was then undulating until the uphill finish, commencing with a third-category climb immediately followed by the first-category Mirador del Sol, a 7 km (4.3 mi) long ascent at an average gradient of 8.75%. It was being used in the race for the second consecutive year as a summit finish, as in 2012, Alberto Contador won ahead of Daniel Díaz, but was later stripped of the result.
27 January 2013 — San Luis to Juana Koslay, 154.7 km (96.1 mi)
The last stage of the race was held over a slightly undulating course which included only one categorised climb; a third-category ascent situated 17 kilometres (11 mi) from the start.
Going into the stage, the mountains classification was led by Emmanuel Guevara, but he had the same amount of points (16) as Alex Correia Diniz, meaning the only categorised climb would determine the winner of that competition. However, neither rider were in a position to score points; thus Guevara won the King of the Mountains competition of the Tour.
The breakaway of the day was composed of eight riders, with Michał Kwiatkowski the best-ranked overall in the general classification, 3' 32" behind race leader Daniel Díaz. Later on, three chasers made the junction, and their lead peaked at 3' 40" with 59 kilometres (37 mi) to go, making Kwiatkowski the virtual leader for a limited amount of time. The teams of the general classification leaders started to work in a concerted effort at the front of the peloton and with 16 kilometres (9.9 mi) to go, the break was nullified. The finishing mass sprint was won by Mattia Gavazzi (Androni Giocattoli-Venezuela), his first victory since returning from a 30-month doping ban; his last victory came at the Settimana Ciclistica Lombarda in 2010. Díaz finished with the main group, and won the overall classification. His team, San Luis Somos Todos, enjoyed other successes; adding to Guevara's mountains victory, Leandro Messineo won the sprints classification.
^Benson, Daniel (23 January 2013). "Diniz climbs to victory in San Luis". Cycling News (Future Publishing Limited). Retrieved 24 January 2013. "This is a huge win for me and for cycling in Brazil...I knew that I had little chance against the World Tour riders if I stayed with them on the climb so I had to go early and try to hang on."