The world number one looked to be cruising at two sets to love but began struggling to move at 4-4 in the third set as the cramp affected his right thigh, but he soldiered on to complete a 6-4, 7-6(5), 6-7(3), 6-7(4), 7-5 win.
Clocking five hours and 27 minutes, it was the longest semi-final at the Australian Open and just shy of the five hours and 29 minutes Alcaraz took to beat Jannik Sinner last year in the longest final at the French Open.
"I think this was one of the more demanding matches that I have played in my career so far," Alcaraz said after improving his record of never losing a match after winning the first two sets to 60-0.
"Physically, we pushed each other to the limit... our bodies to the limit. The level of the fifth set was really high.
"So I'm just really happy to get the win, that I came back. I rank this in the top position of one of the best matches that I have ever won."
Fans were left holding their breath when it appeared like Alcaraz moved towards Zverev to shake his hand after the opening game of the fourth set and call it a day.
But Alcaraz said he did not think about quitting even for a single second despite his woes.
"I hate giving up," he declared.
"I just don't want to feel that way. There are some moments that it seems like, 'OK, I'm giving up' or 'I'm not fighting at all' which, when I was youn,g there were a lot of matches that I didn't want to fight anymore.
"Then I got mature... Just one second more of suffering, one second more of fighting is always worth it. So that's why I just fight until the last ball and always believe that I can come back in every situation."