The Manchester City forward was shown a straight red after losing his bearings and accidentally sending his studs into his opponent's face.
While Mena challenged for the ball with his head, Jesus tried to control it with his boot at speed - and the Chilean was lucky to escape uninjured.
Brazil also got away with one as Chile failed to take advantage of the man advantage for most of the second half and still lost 1-0 thanks to Lucas Paqueta's goal.
Jesus is now suspended for the semi-final against Peru, but the 24-year-old has no complaints, issuing an apology to Mena after the match.
He wrote on Twitter: "Unfortunately I made a mistake in which the team could have suffered, but this group once again showed strength.
"I apologise to my teammates and I will always continue to try to learn from my mistakes. I'm relieved to hear that Mena is fine and we've already talked about it.
"Again, this group is gigantic! We go to the semi!"