Raheem Sterling then scored a brilliant individual goal to seal the victory at St. James' Park.
Speaking after the game, Pep Guardiola was delighted with the win.
"It was a fantastic goal from Raheem," he said.
"For the penalty, I didn't see the review. Gabriel Jesus could have headed the ball and I think the opponent pushed him.
"De Bruyne is definitely reliable and hopefully he can carry on because we struggled a lot this season with this.
"We miss, I think, five or six [penalties]. Kevin now takes responsibility; he has a confident personality and that is important for us."