Del Potro was just 20 years old when he downed the Swiss legend 3-6, 7-6 (7/3), 4-6, 7-6 (7/4), 6-2 but Federer believes that he was the dominant force in that 2009 showdown.
"The only time when he was really better, in my opinion, was the fifth set. Obviously that was good enough to beat me that day," said Federer on Monday after seeing off Philipp Kohlschreiber 6-4, 6-2, 7-5 to set-up Wednesday's quarter-final with Del Potro.
"Feel like I would probably win it somehow because I should have been up maybe two sets to love."
Federer leads Del Potro 16-5 in their head-to-head record although his win in Miami this year represented the first time the pair had met in four years.
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Despite his disappointment at losing the 2009 championship match, Federer admits that having also defeated Rafael Nadal in the semi-finals, Del Potro was overall a worthy winner.
He also became a father for the first time.
"Making the finals here was actually a good run. But it ended my five-year reign in New York," he said.
Federer believes that had Del Potro remained fit he could have become world number one after that breakthrough.
For Del Potro, beating Federer should have meant he had the world at his feet.
Sadly, it was his wrists which proved the problem as he went on to undergo four surgeries.
At one stage last year, his world ranking, once as high as four in the world, slumped to 1,045 and he even considered retiring.
Federer said he was happy to see the likeable Del Potro back on tour and the feeling is mutual.
"I admire him, too. Everybody loves him," said Del Potro.
"It's going to be an interesting match to play. It will be the fitst time after eight years again in the central court of this tournament.
"I know how to play if I want to win, but always is a pleasure to play the greatest guy in history."
He even admitted he had come close to quitting the match as a fever had left him with breathing difficulties.
"I feel tired, but we cannot do magic," he said.
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