"Apologize" earned the band a Grammy Award nomination for Best Pop Performance by a Duo or Group with Vocals and was ranked number 50 on the list of the Billboard Hot 100's All-Time Top Songs list from the chart's first 50 years. It spent 25 consecutive weeks in the Top 10, the longest stay there for any song since "Smooth" by Santana, which spent 30 weeks in 1999. It was also ranked number 10 on the BillboardHot 100 Songs of the Decade. It was OneRepublic's biggest hit single in the United States until "Counting Stars" was released in 2013.
Timbaland remixed the song for his second studio album, Shock Value. This version, also produced by Greg Wells, included an extra line of percussion, new backing vocals, and added sound samples, in addition to sound mixing and various other minor changes. The guitar solo after the second verse was omitted, completing its transformation to a more R&B style to fit with Shock Value. When the remix debuted, on the back of the strong Timbaland name, radio outlets announced the artist for the song as "Timbaland" or "Timbaland with One Republic". As the song gained popularity it was changed to "Timbaland Presents One Republic"
An official video associated with the remix was filmed on September 19, 2007 and released in early October. The video premiered on VH1's Top 20 Countdown on October 27, 2007. The video was directed by Robert Hales and was shot in a recording studio showing OneRepublic performing the song. The video also includes scenes from a New Year's Eve countdown party, starring actor Brian A. Pollack. In a third version of the video, also directed by Robert Hales and associated with the remix, Timbaland is shown remixing the song himself. A European version of the video features clips of the film Keinohrhasen, starring Til Schweiger. A Japanese version of the video was also made available for a short time. It features the same footage as the original but has more scenes from different angles of the camera. It also features footage of people falling and floating in the air in slow motion.
"Apologize" was OneRepublic's breakout hit and first number-one hit. In the United States, "Apologize" peaked at number two on the Billboard Hot 100 for four non-consecutive weeks, first blocked from the top spot for two weeks by Chris Brown's "Kiss Kiss" and then for two weeks by Alicia Keys' "No One". It spent 11 weeks at number three and 25 weeks inside the Top 10 and peaked at number three for 10 weeks on the Hot 100 Airplay. It also topped the Billboard Pop 100 and became the third single from Shock Value to have topped the chart. It also became the album's first number-one single on the BillboardAdult Top 40. It is also the second consecutive single from Shock Value to reach number one on the US Mainstream Top 40 radio. It became only the tenth song to sell over 5 million by May 2011 in the US. As of February 2014, it had sold 5,819,000 copies.
In the UK, "Apologize" climbed to number 32 on the strength of digital downloads alone, and peaked at number three. The song spent 28 consecutive weeks in the Top 40 and 13 weeks in the Top 10. The song ended 2007 as the year's sixteenth biggest selling single in Britain. In Australia, the single debuted at number 10 on the ARIA Singles Chart, and peaked at number one. It stayed at the top for eight consecutive weeks, and was certified 4x Platinum by ARIA. The song reached number one on both the Canadian Hot 100 and New Zealand RIANZ Chart. It is the most downloaded single of all time in Australia and New Zealand. On Billboard 's official European Hot 100 Singles chart, the song debuted at number 16, making it the highest debut chart position of any new act in the history of the chart. It later entered the Top 10. The song went gold in Russia with 100,000 copies sold.
Dutch symphonic metal band Within Temptation covered the song as part of their weekly radio promos for their 15-year anniversary show, Elements. The song is also featured on their cover album The Q-Music Sessions.
Swedish alternative metal band All Ends covered the song on their album All Ends.
A cover version by T.J. and the Revo entitled "Too Late to Apologize: A Declaration", which uses the tune and altered lyrics in the vein of the American Revolution, was produced in 2010 by Soomo Publishing.