The three-time Munich champion won 5-7, 6-0, 6-2 and will take on Italy’s Flavio Cobolli on Saturday for a place in the final.
Zverev burst out of the blocks and served for a 5-1 lead in the opening set, but appeared to suddenly lose his rhythm, winning just one more game as Cerundolo powered back to take the opening set.
As the second set began, and with the support of the home crowd, the 28-year-old found his form as swiftly as he had lost it, bouncing back to win the final two sets while dropping just two games.
“Even in the first set when I was up 4-1, he started playing unbelievable. He started returning unbelievable,” Zverev said.
“My first-serve percentage was very high, and he started returning a foot in front of the baseline. So there was nothing I could do, to be honest.”
The German came into Friday’s match holding a 4-3 career advantage over the fifth-seeded Cerundolo but had never previously beaten the Argentine in three matches on clay.
“Definitely happy to get the win today against Francisco, for the first time on clay,” Zverev said on court after the win.
Zverev, whose most recent title came in Munich a year ago, is chasing a record fourth triumph at the tournament, having also won in 2017 and 2018.
On the other side of the draw, American second seed Ben Shelton overcame Brazilian teenager Joao Fonseca to keep hopes of a 2025 Munich final rematch with Zverev alive.
Shelton, the world number six, won 6-3, 3-6, 6-3 and will take on Alex Molcan in the semi-finals, with the Slovak continuing his fairytale run at the tournament by beating Denis Shapovalov 6-4, 6-4.
Shelton has never won a clay court tournament, having lost in straight sets to Zverev in Munich a year ago.
Earlier, Cobolli was the first to book a spot in the final four after he defeated Czech Vit Kopriva 6-3, 6-2.
Playing on his favourite surface, the fourth seed won the opening set and cruised to a 5-1 lead in the second. He missed two match points on Kopriva’s serve before finishing it off in the following game.
Follow the Munich tournament with Flashscore.
