Federer, 35, who had a surprise first-round exit at Stuttgart, was in a superb form as he didn?t even lose a set in the entire tournament.
Federer won the first meeting between the two on the clay courts of Rome in 2016, winning in straight sets, but the pair's second meeting at Halle previous year at the semi-final stage was won by Zverev, which he won in three sets.
Zverev managed to hold his serve at the third opportunity, but Federer broke again at 5-1 to claim the first set in just 22 minutes.
Zverev will also be a player to watch during Wimbledon.
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. Federer triumphed in their first meeting on clay in the 2016 Italian Open with a straight set win in the round of 32 while Zverev got a win in the 2016 Halle Open semi-final.
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Swiss great Roger Federer thrashed Alexander Zverev to win his ninth Halle title on Sunday and admitted he's feeling fresh ahead of his assault on an eighth Wimbledon crown next month. Federer is a seven-time victor at Wimbledon and must be considered a favorite at the major tournament.
During the second set, Federer survived a break point in the opening game before taking a 4-2 lead with a signature backhand volley.
Federer was on top of his game and didn't allow Zverev to make a comeback and took the first set in 24 points after earning a second break point.
Twenty-year-old German Alexander Zverev defeated Richard Gasquet at the Halle Open in Germany on Saturday. "He could have been a little nicer to me", Zverev said.
Federer did not participate in the French Open after winning back to back titles, starting from the Australian Open, Indian Wells and then Miami. "So I'm happy to react right away and let that be forgotten and actually move on and remind myself I actually can play well on grass".