He will next face Karen Khachanov, who defeated Andrey Rublev 7-6 (8), 4-6, 6-3.
But, instead of serving out the set, the top seed was broken again and Khachanov even held two set points at 6-5 before the world No. 5 recovered and forced a tie-break.
While Federer enters Sunday's final without dropping a set, Zverev saw off French veteran Richard Gasquet 4-6, 6-4, 6-3 in the semi-final. Zverev meanwhile has been in the form of his career in 2017, having won three tournaments including his first Masters 1000 victory by beating Novak Djokovic in Rome.
The dream final was set in Halle Saturday as Roger Federer and local wunderkind Alexander Zverev advanced to a tasty title match tomorrow.
He lost in the opening round of the Mercedes Cup in Stuttgart last week to Tommy Haas but has looked much more impressive in Halle which is ominous for his rivals ahead of Wimbledon, which starts on July 3.
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Italian Open champion Zverev had won all three of his previous finals this season, but was blown away by a vintage performance from the 18-time major champion in only 53 minutes.
" Marin has been playing unbelievable and is also a great grass-court player, so I think I have to play my best tennis if I want to win", he said.
A trademark forehand passing shot and a comfortable service game moved Federer to within a game of victory. I'm very happy for him, how he's developed in the last years.
Federer surprisingly donated serve once in each set, but a second break of his own allowed him to take the first and he was extended to a tiebreaker in the second.
"It's tough to play against a friend like Lucie", Kvitova said.
"I played against a right-hander from the baseline in Sugita, a left-hander who serves and volleys all time (Zverev) and Mayer plays very differently to everyone else". "I do not know if I will ever be going to win this tournament again so I will enjoy this one".