It was Federer's third title success in the Hopman Cup, more than any other player, following victory in 2001 alongside then World No.1 Martina Hingis and last year's win with Bencic.
Federer had a straight sets 6-4, 6-2 win over Alexander Zverev but his hard work only to be lost when Angelique Kerber defeated Bencic in the women's singles 6-4, 7-6.
Ferrer, who will be retiring at Madrid in May, defeated Lucas Pouille 6-4, 6-7 (5), 7-6 (2) in Spain's final round-robin tie.
Federer first won the Hopman Cup back in 2001 against the USA when he paired with Martina Hingis.
Stefanos Tsitsipas and Maria Sakkari had one of the best evenings of their young careers.
Federer's 2019 tennis season has gotten off to the strongest possible start as he helped Switzerland retain the Hopman Cup this week.
The German's serve is big-and here he maintained a near constant speed of over 200kph-but the more nuanced and accurate serving of Federer ensured the Swiss dropped only two points on his serve in the entire first set. A tight encounter saw Greek pair take the first set 4-3 lead.More news: Georgia quarterback Justin Fields transferring to Ohio State
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Zverev broke his opponent's serve three times - the first coming in the third game of the first set after some aggressive tennis.
"We only got to the final a year ago because of Angie". But the Swiss, nearly as quickly, hit back with a hold and break for the loss of one point, and then worked three break chances, as Federer hovered courtside taking photos. "I'm a bit surprised that the matches have gone as well as they have", he said.
It was not until Kerber's third match point that a backhand victor secured the 6-4, 7-6 (8/6) win.
Kerber had two match points at 6-4 in the tie-break, but Bencic again hung on grimly and won the next two points.
Critical to the result was Kerber's ability to convert all four of her break points during the match, while Bencic was only successful on two of seven.
"I'm happy I'm feeling this good and playing as well as I am", Federer said. Now with back to back wins at the event, Team Switzerland appears unstoppable.