The 18-times grand slam champion, who skipped the claycourt season to prepare for grass after winning the Australian Open and titles in Indian Wells and Miami, is in ominous form and won in Halle without dropping a single set all week.
"It has been a difficult year with a lot of practice, training and rehab so I am very happy to be back on the court," Federer said.
"I do not know if I will ever be going to win this tournament again so I will enjoy this one," said the Swiss, who has won eight Wimbledon titles.
The 35-year-old, defeated in his first comeback match in Stuttgart last week, took control from the start with an early break and kept world number 12 Zverev on his toes.
He earned a second break point with some deft volleying, which he pounced on to race through the first set in 24 minutes.
Zverev, who beat the Swiss in last year's semi-final and has already won three titles this year, had a chance to break at the start of the second set.
But he simply could not discover a chink in Federer's armour, even as he attempted to mix up his game by forcing the Swiss to come to the net more often.
A superb dropshot put Federer 5-2 ahead and sealed Zverev's fate before he won the match on his first match point with a crosscourt volley.
In doing so, he became the first player to beat both Zverev brothers at the same event, having defeated older sibling Mischa in the round of 16.
(Reporting by Karolos Grohmann; Editing by Toby Davis and Brian Homewood)
