Meanwhile, Federer became the most successful player in Hopman Cup history when he led Switzerland to a 2-1 win in an enthralling final of the mixed teams tournament.
Although the 6-4, 6-2 win over Zverev in the Hopman final reversed a loss to the German in London in November, Federer said he was just one of many challengers in Melbourne.
The Swiss pair then clinched the trophy with a 4-0 1-4 4-3 doubles win that went to the final winner-takes-all point.
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"It's nice to be back in the final and play Switzerland, who we lost to in a very close match previous year", he said.
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. However, Zverev and Kerber returned fire, taking the second set from the Swiss combo 4-1.
Zverev had a glimmer of hope in the first game of the second set, 0-30, and two deuces, but the Federer serving was just too good.
Zverev saved one break point in the eighth game, Federer claiming the first set after the German netted a backhand at 15/40 in the 10th game.
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The German served at 5-4, but the match took a sudden twist as Bencic broke back, only for Kerber to immediately break again. "I'm a bit surprised the matches have gone as well as they have", the 37-year-old added.
Roger Federer will go down as possibly the greatest tennis player of all time.
It was Kerber who maintained her 100 per cent record in the competition, triumphing 6-4 6-4 before Zverev earned a 6-4 6-3 win over Ebden.
A new ATP World Team Cup tournament is set to be introduced in Australia next year, with the Hopman Cup nearly certain to make way for the 24-team event.
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"I'm very happy. That was always the goal to get to the final", Federer said. American superstar Serena, who was playing in Perth for the fifth time in her career and has won the title twice, said she was unaware of speculation on the Hopman's fate, but that she was upset by the prospect of it vanishing.