The spot kick was awarded after Bo Svensson's shot appeared to hit Manuel Friedrich's hand, although there looked to be no way the defender could have got out of the way.
"It's controversial to say that Manuel Friedrich handled the ball in the area," Tuchel told reporters.
"I would say it's a case where the penalty should not have been given. But I have to also say that I no longer know when a penalty should be given and when a penalty shouldn't be given."
"I can't explain it any more."
Mainz midfielder Andreas Ivanschitz, who converted the kick, agreed it was not a penalty but said they were due some luck.
"We have had some penalties not given to us in the last few weeks," said the Austrian. "I don't think the penalty had to be given but it evened things out for us."
Leverkusen sporting director Rudi Voeller said the penalty should not have been given under any circumstances.
"That was not a penalty in the past, it is not a penalty today and it will not be a penalty in the future," said the former Germany coach and forward.
Bayer are third in the Bundesliga six points clear of fourth-placed Schalke 04 in the race for an automatic spot in next season's Champions League.