Cruz appeared to be in control of the bout as the fighters headed into the championship rounds, with the judges putting him ahead 2-1.
However, Vera landed a brutal head kick in the fourth round, dropping Cruz to the canvas. Vera pounced to follow up with punches, and experienced referee Herb Dean intervened to stop the fight seconds later.
Cejudo believes Cruz was unlucky not to come away with the win after an impressive performance in the opening rounds.
"That's the name of the game," Cejudo said, as quoted by MMA Junkie.
"Dominick was winning the fight for four rounds to zero before he got clipped with that head kick. 'Chito' was never in trouble, but he was getting outstriked, you see what I'm saying?
"Yeah, he knocked him out. But if you look at the whole fight, Dominick was peppering that dude. But 'Chito' did win."
Vera now boasts a 14-6 record in the UFC, while Cruz is 7-3.