Federer was simply irresistible in his singles match, countering the power of Zverev with classy stroke play and unpredictable deftness.
Earlier Federer withstood a serving barrage from Zverev to give Switzerland a 1-0 lead in the tournament decider.
World No. 2 Kerber appeared set for an easy win in her singles match against Bencic, taking the 1st set and then claiming an early break in the 2nd.
Bencic looked to close out overall victory for Switzerland, but Kerber levelled up the final with a commanding 6-4 7-6 (6) win.
Federer also became the first player to win successive Hopman Cups and said the records were a nice bonus for winning the title.
The victor of the final round robin tie would advance to Saturday's final against Swiss defending champions Roger Federer and Belinda Bencic and it was the Germans who prevailed by claiming both singles matches.
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Federer said the win helped atone for a loss to the German in the semi-finals of the season-ending ATP World Tour event in London. I'm OK either way, but this was not to get a racket from her, this was just a spontaneous 'Why don't you keep the racket?' because her coach had already taken all her bags off the court, which I couldn't believe.
"I'm very happy about these records, but I didn't come here for that", 20-times major champion Federer said.
"I think he's the favourite, regardless of what happened in Doha, the guy had a super, super strong last five, six months of the year", said Federer.
"Winning it back-to-back years, what a thrill it was, not just the match point but the whole week".
"She did it", the Swiss star said, blaming Bencic for making him laugh. "It's been a super pleasure teaming with Belinda". I hope we can come back here many more times.
"It is good to finish on a singles performance like this, I was able to come up with some good serve and volley and it all worked out today".
"It was a good match for me, no doubt about it", he said.
Previous year he won his first 21 matches of the season, including the Australian Open title, as he became the oldest player to ever hold the number one ranking.