Pitroipa, one of Burkina Faso's best players in their unlikely advance to the final, was sent off late in extra time of the Stallions' semi-final penalty shootout victory over Ghana after he was shown a second yellow card by Tunisian referee Slim Jdidi for diving.
But Confederation of African Football officials ruled on Friday the winger could play in the final after Jdidi admitted making the wrong decision and booking him by mistake.
"I applaud the decision taken by CAF," Keshi told reporters at his pre-match briefing on Saturday.
"It was obvious Jonathan did not deserve a red card and I think it is good for the game that Jonathan is playing, so I am happy. It is good for the final. There will be a sellout crowd and they want to see the best players.
"It is not every day that you get the chance to play in a final, and denying him that chance would have been very tough."
The two sides are meeting for the second time in the tournament after drawing their opening group match 1-1 nearly three weeks ago, when Pitroipa created Burkina Faso's late goal for Alain Traore.
Keshi said his planning for the final would be helped by having already played the opposition in the group stage.
"I think it is more benefical, because we didn't know Burkina Faso before that game, and maybe they didn't know us," he said. "But we have learnt from the mistakes we made in that game, and now have to prepare for the final accordingly."
While Keshi will have to worry about Pitroipa's attacking forays, he also has concerns closer to home.
His key striker, Emmanuel Emenike, who has scored three goals in the tournament, is a doubt with a thigh strain. Forward Victor Moses, outstanding in the 4-1 semi-final win over Mali, is nursing an ankle injury.
Keshi said he would decide on his line-up on Sunday morning, adding, "They are not 100 per cent, but perhaps if they are 80 per cent fit, that might be enough for me".
Nigeria last won the title in 1994, when Keshi was a player. If they triumph on Sunday he will become only the second man in the 56-year history of the tournament to win it as both player and coach.
Asked what that would mean to his CV, he replied: "It's not about me, this is for all Nigerians."
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- Burkina Faso