Del Potro, who has bounced back from a series of wrist injuries, clinched his first Masters title after winning an epic three-setter 6-4, 6-7, 7-6.
Federer, who recorded his best ever start to a season when he clinched his 17th straight win in the semi-final against Borna Coric, wasted three Championship points.
But the Swiss legend had nothing but praise for his opponent after letting the result sink in.
“What a battle today,” he wrote on Twitter.
“Congrats on a fantastic tournament and match, @delpotrojuan.”
The love in between the two players started during Del Potro’s victory speech when he praised Federer’s continued impact on the game of tennis.
“I’m still shaking, I think this is the worst part for me,” he said.
“First of all I want to congratulate Roger to a great week and great success in this historical year.
“You’re making history and I’m so happy to be just behind you, seeing what you do.
“It’s amazing for our sport and for the life so thank you very much.”
In his loser’s speech, Federer told Del Potro to “enjoy the moment” after his struggles with injury.
“Juan Martin well played today,” the 36-year-old said. “It was a tough match, but well done you deserve it.
“There was not much between us, but you deserved it.
“Well done and enjoy the moment.”
