The captain was initially ruled out for two weeks but has not played since, with Bayern keen not to rush him back into action.
However, Neuer trained this week and Kovac revealed the World Cup winner will be back between the posts against Leipzig in Berlin.
"I can say Manuel will play," the coach told a news conference on Friday. "He is our captain and has done well this season. He is a cornerstone of our team."
Saturday's match will be the last opportunity for departing stars Rafinha, Franck Ribery and Arjen Robben to feature for Bayern.
However, Kovac insists he cannot allow that to play into his thinking when it comes to team selection.
He said: "It will be the last competitive match for these three top players, but we have a very difficult task - as we did against Eintracht Frankfurt [in the Bundesliga last weekend].
"It will be a very difficult decision for me, because I know how hard it is. But we have players who did a great job in the second half of the season, so I have to give them the confidence that they deserve.
"I can only choose 11 players, but everything is possible [on Saturday]. Everyone can play - even the three that are leaving Bayern."
Kovac and Bayern CEO Karl-Heinz Rummenigge have insisted he will remain as coach next season, yet the former Frankfurt boss was not willing to discuss his future.
"We have a cup final ahead of us," he said. "We should talk about football. I want to throw all my energy into the team and the job. My future is secondary."