They were set against each other in the World Music category of the US music awards on Sunday night.
But Kidjo won, for the fourth time, leaving Burna Boy still waiting to win his first.
She said that he is changing Africa:
"Four years ago on this stage, I was telling you that the new generation of artists coming from Africa are going to take you by storm.
"And the time has come. This is for Burna Boy.
"Burna Boy is among those young artists that come from Africa that is changing the way our continent is perceived and the way African music has been the bedrock of every music."