Defender Santiago Ostolaza headed the winner in the 74th minute to take Racing level on seven points with leaders Corinthians of Brazil in Group One. The pair are now firm favourites to progress to the knockout stages.
Medellin, who had forward Edison Gimenez sent off in the 84th minute for punching an opponent, are in third place on three points with only two games to play.
Racing have never won the Uruguayan championship and spent long periods in the second division. Some 3,000 fans watched the game in Montevideo's huge Centenario stadium.
Argentina's Velez Sarsfield came from behind to beat Chile's Colo Colo 2-1 in a meeting of former champions in Group Seven.
Michael Arroyo gave Deportivo Quito a 1-0 win at home to fellow Ecuadoreans Emelec in Thursday's other match, condemning their opponents to a third successive defeat in Group Five.
