Federer, who has put in commanding performances for his country in Perth, was sublime again as he brushed aside the 21-year-old World Tour Finals champion with a 6-4 6-2 win.
It all came down to a thrilling mix doubles with the Swiss coming up trumps 4-0, 1-4, 4-3.
Federer will be aiming for a third successive Australian Open and looked in impressive touch in claiming a second Hopman Cup, winning all four of his singles matches as he prepared for the year's first Grand Slam in Melbourne later this month.
Federer, who also beat Zverev in 3 sets in last year's Hopman final, clinched the match with a typically crisp forehand volley.
Bencic started the second set just like the first, offering a break in the first game, but hung on through deuce for 2-3.
Federer said Djokovic is "hard to beat" and has enjoyed a remarkable last six months.
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.
Zverev, beaten in the final two years in a row, said he hoped there would be a chance to atone and that he hadn't played his last Hopman match.
While tennis fans across the globe will never grow exhausted of watching Roger Federer triumph, the novelty has well and truly worn off among the Swiss maestro's rivals. Bencic sealed a final love break of Kerber with a forehand victor, 4-0.
"I'm happy I'm feeling this good and playing as well as I am", he said.
They, therefore, went down in the tight mixed doubles rubber.
Tsitsipas played a fantastic match against Federer, but eventually he lost 7-6 (5) 7-6 (4).
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.
A new ATP World Team Cup tournament is set to be introduced in Australia next year.
Osaka kicked the air at one point and dropped her racket to the court after missing another, before visibly questioning how she could be getting it so wrong when her forehand skewed wide on game point.