Jesus broke the deadlock after 34 minutes, with City's passage to the knockout stages already secured.
The Brazilian then added two more shortly after half-time before Phil Foden capped off the victory with six minutes remaining.
Speaking after the game, Jesus said: "I didn't see the player on the floor I'm on the back [to the incident]. I want to say sorry because I didn't see.
"I enjoyed it, all the time I score goals I enjoy. I'm happy with my teammates, they help me.
"It's special, when I'm young I think about playing and scoring in the Champions League so it's very special to score goals and a hat-trick as well."