The Burkinabe forward was booked for simulation, and subsequently sent off but replays showed he was clipped.
Keshi, whose Super Eagles play Pitriopa's Stallions in Sunday's African Nations Cup Final, says CAF did the correct thing.
"I applaud the decision taken by CAF because if you look at the video, he didn't deserve a red card," Keshi said.
"Playing in a final doesn't come very often, and to deny him the chance to play is unfair. I'm very happy for Jonathan."
Keshi was also pleased that fans would get a chance to see one of the continent's best players on show.
"And it's also good for the fans. Because you don't want to pay money and not watch the best players."
The Nigeria coach insisted however, that his preparations for the game have not been affected.
"No, we have continued to prepare the same way."