Kerber managed with a 6:4, 7:6 (8:6) how twelve months ago the balance in the duel with Bencic, who is now number 18 in the world rankings.
Switzerland then came up trumps 4-0 1-4 4-3 (5-4) in a deciding mixed doubles clash that came down to the final point.
Federer's performance-level was "the flawless preparation for the Australian Open", according to CNN, and the 20-time Grand Slam champion himself described "the whole match and the whole week" as one giant "thrill".
Federer, who also beat Zverev in 3 sets in last year's Hopman final, clinched the match with a typically crisp forehand volley.
Barty had four chances to break back in the fourth game of the second set, but Kerber battled valiantly to hold serve. But Federer and Bencic hit back in the second to ensure a tie.
But Federer snared the crucial break in the 10th game of the first set, before breaking the young German again early in the second set on the way to the 70-minute win.
The 37-year-old said he was pleased with the victory which put the Swiss pair in the box set to defend their title.
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After overpowering a stubborn Ebden, Zverev said he and Kerber were motivated by last year's loss in the final.
"It was a good match for me, no doubt about it", he said. But in the end, the experience and athleticism of Kerber proved just enough to seal the match, 7-6 (6), with a final victor.
Federer said it is a great start to the summer.
They changed ends at 3-3, with their partners both watching intently from the side-lines, and Bencic saved two match points to change ends still all square, 6-6.
The final against Germany was settled by a tense mixed-doubles rubber that went to a tiebreak.
Serena Williams, who has won the Hopman Cup twice in her five appearances, said it would be "heartbreaking" if the mixed-team event was axed as women would not be involved in the World Cup.
While Tennis Australia has a contract with the West Australian State Government to run the ITF-sanctioned tournament until 2022, the new ATP event would make it very hard for the Hopman Cup to attract top men's players.