The 18-times grand-slam champion, who captured the Australian Open, Indian Wells and Miami titles this year, skipped the entire claycourt season to improve his chances of winning a record eighth title at the All England Club.
He will now face 20-year-old Zverev in a rematch of last year's semi-final, which the German won. Zverev booked his second successive final spot when he beat Frenchman Richard Gasquet 4-6 6-4 6-3.
Gasquet, a two-time Wimbledon semi-finalist, grabbed the first set against Zverev with a break at 5-4.
But he quickly fell behind in the second as Zverev, a finalist last year, who has already won three titles in 2017, charged to a 4-2 lead and held on to take the set.
The world number 12 booked his final spot after breaking at 3-3 and finishing the Frenchman off with another break to set up the showdown with Federer.
Despite a shock exit from Stuttgart on his comeback last week, Federer has improved in Halle and has not lost a set.
"I thought it was extremely close, especially that second set," Federer, who has never won a tournament nine times, told reporters.
"I'm still just very happy how I was able to close it out in the (tie-)breaker," said the 35-year-old.
He and Khachanov, 21, traded breaks in the first two games but Federer grabbed a second one to restore his advantage and clinch the first set on his second set point.
The Swiss lured the youngster to the net on several occasions, including at 4-4 in the second set when the Russian dumped a forehand volley into the net to give Federer two break points.
But instead of serving out the set, the top seed was broken again and the Russian even held two set points at 6-5 before the world number five recovered and forced a tiebreak.
He converted his first match point to reach an 11th Halle final.
(Reporting by Karolos Grohmann, editing by Pritha Sarkar, Neville Dalton)
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