Dida hurt his right shoulder during last Wednesday's first leg in Quito, which the Brazilian club lost 0-1 after a late goal by Carols Feraud, reports Xinhua.
He will be replaced for the return match in Porto Alegre by Marcelo Grohe, Gremio officials confirmed Friday.
"This is the game of the year for us because we have to win to keep our Copa Libertadores hopes alive. The home fans are going to help us and with their vocal support we are going to do all we can to qualify," Grohe said.
Gremio, coached by former Brazil and Real Madrid boss Vanderlei Luxemburgo, needs to win by a minimum of two goals to advance to the tournament's group stage.