Everton had earlier given Cruzeiro a 2-1 lead after Martinuccio cancelled out Bernard's opener for Atletico at the Arena Independencia in Belo Horizonte Sunday, reports Xinhua.
Ronaldinho tapped in at the far post early in the second half after Marcos Rocha's corner was headed goal-ward by Leonardo Silva.
The former Barcelona and AC Milan star then set up Rever's winner with a pinpoint free-kick which the former Wolfsburg defender headed beyond the reach of goalkeeper Fabio.
After the match Ronaldinho said the club would savour celebrating its first Copa Libertadores berth since 2000.
"It's going to be a great celebration and the fans deserve it. It's been too long since our last appearance in the Copa Libertadores," Ronaldinho said.
"It was a great year but we want 2013 to be even better. We have to make the most of our time off and then turn our focus towards having an excellent season next year."
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In other games, Vasco da Gama defeated champions Fluminense 2-1, Sao Paulo overcame Corinthians 3-1 while Gremio drew 0-0 with Internacional.