Wimbledon champion Kerber saved four break points in the second set to beat an error-prone Ashleigh Barty 6-4 6-4 to set the ball rolling for Germany on Friday, before Zverev swatted aside Matthew Ebden 6-4 6-3 to seal the win.
The Swiss pair wrapped up the tournament decider in the mixed doubles 4-0 1-4 4-3 (5-4) in the most exciting final of the event's 31-year history.
The 37-year-old used the Hopman Cup as his launching pad for winning the past two Australian Opens, the first of which in 2017 ended an nearly five-year Grand Slam drought for Federer.
"Winning back to back Australian Opens in my 30s has been one of my favourite things I'll look back on", Federer said.
"I was playing point by point, not thinking too far ahead and just going for it".
With the tournament now in the balance at 1-1, it all came down the mixed doubles pairing.
The 31st edition of the mixed-teams tournament has been its best one, featuring record crowds and attracting worldwide interest when Serena Williams played mixed doubles against Roger Federer. "We were disappointed last year and sworn in this year, we wanted to win".
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The 37-year-old Swiss superstar surprisingly ended up losing out to the Greek couple and handed the very young stars a flattering win in their early careers that they will truly never forget.
But the event appears doomed, due to the creation of a new ATP World Team Cup, which is set to be launched in Australia from January 2020.
Federer defeated Frances Tiafoe, Stefanos Tsitsipas, Cameron Norrie and Zverev in straight sets and will be full of confidence heading into Melbourne Park later this month.
And also just one poor service game in the first set - there wasn't really much in it in the end.
Kerber leveled with a 6-4, 7-6 (6) win over Bencic.
"It was a good Match for me, no doubt about it", he said, and stressed: "I have well-pitched". "So I think like that was sort of my main problem today".