World number one Alcaraz was struggling to move at 4-4 in the third set and was allowed treatment on his right thigh at the change of ends, leaving German Zverev incensed.
Zverev was adamant that Alcaraz was struggling with cramp, which is out-of-bounds for medical timeouts.
Alcaraz dropped the next two sets but was back running at full pelt in the fifth to close out an epic 6-4, 7-6(5), 6-7(3), 6-7(4), 7-5 win in five hours and 27 minutes.
"Yeah, I mean, he was cramping, so normally you can't take a medical timeout for cramping," third seed Zverev said at his post-match press conference.
"What can I do? It's not my decision. I didn't like it, but it's not my decision."
On court, Zverev lashed out at a match supervisor in profanity-laden German as Alcaraz underwent treatment.
"I just said it was bullsh*t, basically," he said later of the exchange, noting that Alcaraz finished full of running.
"He took like an hour and a half off, where he wasn't moving almost at all, so again, maybe I should have used that better in a way. Maybe I should have won the games and won the sets a bit quicker.
"Then moving into the fifth, maybe he wouldn't have had so much time to recover. But the fifth set, the way he was moving, was incredible again."
Runner-up to Jannik Sinner last year, Zverev was serving for the match at 5-4 in the fifth set of Friday's semi-final but Alcaraz won the next three games to leave the German with another near-miss at the Grand Slams.
Still chasing an elusive first major title, Zverev said he had more regrets about dropping the second set than his surrender in the fifth.
"I was hanging on for dear life, to be honest. I was exhausted," he said, rating the match as probably the toughest physically of his career.
"I think we both went to our absolute limits, so somewhat I'm also proud of myself, the way I was hanging on and came back from two sets to love.
"Of course it's disappointing but this is the start of the year, so if I continue playing that way, if I continue training the way I train, if I continue working on the things that I've been working in the offseason, I do believe it's going to be a good year for me."