The world number three had earlier shown why he is a firm favourite for the season's first major, firing 24 winners and nine aces in a flawless 6-4 6-2 victory over ATP Finals champion Zverev.
Kerber too maintained her 100 percent singles record with a 6-4 7-6(6) victory over Bencic to level the tie at 1-1, but the Germans failed to make the most of their opportunities as they went down in the tight mixed doubles rubber.
"I'm happy I'm feeling this good and playing as well as I am," said Federer, who has won the last two Australian Open titles after taking part in the mixed-team event.
Federer has beaten Frances Tiafoe, Stefanos Tsitsipas, Cameron Norrie and Zverev in straight sets and will be full of confidence heading into Melbourne Park later this month.
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"It's good to finish on a singles performance like this. I'm a bit surprised the matches have gone as well as they have," the 37-year-old added.
It was Federer's third title success in the Hopman Cup, more than any other player, following victory in 2001 alongside then world number one Martina Hingis and last year's win with Bencic.
Federer and Bencic are also the first pair in the event's 31-year history to retain their title.
"I'm very happy about these records, but I didn't come here for that," 20-times major champion Federer said.
"What a thrill it was – not just the match point but also the whole match and the whole week. It's great fun.
"I'm happy, I'm proud to represent my country. It's been a super pleasure teaming with Belinda."
Switzerland's first win in the competition was secured by Manuela Maleeva-Fragniere and Jakob Hlasek in 1992.
(Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Ken Ferris)
