Hewitt raced through the first set and then held off a comeback from the world number six to win 6-1 4-6 6-3 in two hours and seven minutes.
It was Hewitt's 29th title on the ATP tour but his first since 2010, when he also beat Federer in the final at Halle.
Hewitt has been plagued by injury in recent years and underwent surgery in 2010, 2011 and 2012 to fix various hip and foot problems.
"I think the most pleasing thing is what I've had to come through and the tough times in terms of surgery," the former Wimbledon and US Open champion said.
"There were still times when I came back from that surgery and played that Wimbledon straight after it, and I was still doubting whether I was ever going to be pain-free again.
"For me that's the most pleasing thing."
Hewitt, the world number 60, is projected to rise to 43 in the rankings as a result of the win, and will be one of the most dangerous floaters when the Australian Open draw is made on January 10.
However, Federer denied the high workload was to blame for his performance despite looking fatigued at times.
"I feel actually pretty good considering playing five sets yesterday and coming out and playing another three-setter today, (considering) the warmer weather the last couple of days in particular," he said.
The Swiss great had not lost his serve all week, but he appeared sluggish from the beginning and was broken to love in the first game.
"I wouldn't say I was serving poorly, but it was just a tough set for me. I was put on the back foot very often.
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