Leandro Caruso put the hosts ahead eight minutes into the game, only for a Luis Fernando Mosquera brace to turn things around for Atletico. The Argentinian team were back level by half-time, though, thanks to Ruben Ramirez's strike.
Two goals from Dorlan Pabon twice then saw the visitors take the lead after the interval, but both were cancelled out by Godoy Cruz striker Caruso as he completed his hat-trick.
"We committed many mistakes and we have to correct them if we want to advance to the next stage," Godoy Cruz head coach Nery Pumpido said. "But, despite all those things we did wrong, our chances are still intact."
Atletico Nacional moved on to seven points at the pool summit, with Godoy Cruz in second place alongside Chilean giants Universidad de Chile on four points.
Elsewhere, Brazilian side Flamengo secured a 1-0 win over Ecuador's Emelec in a Group Two match in Rio de Janeiro. Vagner Love scored the game's only goal with a cross-shot from Ronaldinho's pass.
It was not all positive for Ronaldinho, however, with the home fans booing the former Barcelona and AC Milan forward at the end of the match.
Coach Joel Santana said: "Maybe the supporters think the one-goal difference is a poor performance, but we can't win all the games by four or five goals. Libertadores is a hard tournament."
Despite the fans' reaction, the win took Flamengo top of Group Two on four points - one ahead of Paraguayan team Olimpia and Emelec.
Finally, Bolivia's Bolivar secured a surprising 1-0 win against Junior thanks to an 80th-minute header by William Ferreira in Barranquilla.
The result saw Angel Hoyos' side move on to four points in Group Three and up to second place - three above Chilean side Union Espanola and one ahead of Universidad Catolica and Junior.