Alou was considered a better prospect than either of his brothers and received a $4,000 signing bonus. He made his debut at the end of 1963, and his first game, on September 10, was notable in that all three Alou brothers batted in the same inning (they were retired in order). Five days later, for the first time, the three played in the outfield for the Giants at the same time.
In his first full year of Major League action in 1964, Alou failed to live up to expectations, hitting only .274 with little power, but on July 10, he went 6–6 with five singles and a home run. Alou was selected by the Montreal Expos in the 1968 MLB expansion draft and then was dealt to Houston. He had his most active season there, hitting .306 in 487 at-bats, but with few walks and little power. He was traded to the Athletics midway through the 1973 season, and served as a bench player on two World Series championship teams. Alou was released by the A's before the 1975 season, failed to catch on with the Mets and Cordoba of the Mexican League in short stints, and did not return to the majors until Houston signed him in 1978. He responded by hitting .324 in part-time action and became a player-coach the following year before retiring. Alou later served as a scout for the Expos, then moved to the Florida Marlins as the club's director of Dominican operations. He has held the same post with the Boston Red Sox since the 2002 season.