The victory secured the team from Mendoza's place in South America's elite club competition alongside Boca Juniors, Velez Sarsfield, Arsenal and Lanus.
Boca, who have won the title six times and four since 2000, qualify as winners of the Apertura championship that finished on Monday and Velez as champions of the Clausura that closed last season in June.
Arsenal went through as Argentina's best-placed team in the 2011 Copa Sudamericana, the region's second tier club competition.
Lanus and Godoy Cruz are the two best teams on points over the calendar year, which spans the second half of one season and the first half of the next and is used to decide which teams go through.
Record seven times South American champions Independiente did their best to try to qualify with a 2-1 home win over Tigre but they needed Godoy Cruz to lose.
Godoy Cruz, who had been struggling for weeks, went into the match with a run of three defeats and a draw and only one victory in their last eight.
Midfielder Ariel Rojas, the man of the match, put them ahead five minutes before half-time and striker Ruben Ramirez, who took his tally as the Apertura's top scorer to 12 goals, made the result safe in the 72nd minute.
"[Going through] depended on us. We've finished a good year in which we played the Libertadores and Sudamericana. We have a very good squad," midfielder Diego Villar told reporters.
Coach Jorge da Silva's team finished with 10 men as midfielder Israel Damonte was sent off for a second booking a minute after their second goal.
Boca, unbeaten in 29 matches going back to last season, finished the 19-match Apertura with 43 points, 12 more than a group of four teams, Velez, Racing, promoted Atletico Belgrano and Colon, on 31 points.
