However, 21-year-old Khachanov rallied and force two set points which would have taken the match into a decider before Federer, an 18-time Grand Slam victor, closed out the tie-break.
This will be the second meeting between Federer and Zverev in the Halle Open after the latter triumphed in a 7-6, 5-7, 6-3 semi-final win.
However, the Swiss ace will have to get past the talented Zverev.
All Offers and Promotions posted in this article excludes NSW residents.
It's also worth noting on the two other occasions he made the final in Germany and lost (2010 and 2012) - he reached the quarter-finals at Wimbledon (Losing to Tomas Berdych) and won two years later (Beating Andy Murray). He's playing really good tennis.
This was the ninth Halle title win for the 18-time Grand Slam champion.
Federer, who hit 11 aces and 32 winners, said facing Khachanov, who he has never played previously - at least competitively, will present a new challenge for him.
Federer and Nadal lead the ATP Tour this year with four titles each - Nadal's most recent coming in Paris, where he became the first player in the post-1967 era to win a single grand slam 10 times.
The 35-year-old broke in the opening game of the match to establish his control and did not offer a reprieve as he dominated from start to finish. The Russian then missed two set points before Federer took it to the tiebreaker. At 35, the Swiss player became the oldest victor of the grass-court tournament. It was quite quick, and usually in doubles the points are a little bit shorter.
Speaking at the post-match presentation, Federer said: "It's been a hard year - we had a lot of practice, a lot of training, a lot of rehab to do, so it's nice to be back on the match courts and it feels great". It pits world no. 5 Roger Federer against the word no. 12 and home favourite, and one of the rising stars in world tennis in 20-year-old Alexander Zverev.