Federer, who won his fourth Miami title, broke Isner three times in a blazing opening set.
"It was a dream start, relaxing my nerves," the Swiss, 37, said in a courtside interview.
But the American fought back in the second, levelling the set at 3-3 and 4-4 before the pain made it difficult to continue. Federer took the final two games for the victory.
"What a week its been for me," said the fourth seed. "I'm just so happy right now. It's unbelievable. I played here in 1999 for the first time and here I am in 2019. It means a lot to me."
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Only American Jimmy Connors, with 109, has more career singles titles than Federer.
Isner began to feel pain in the first set.
"I started feeling some pain on the top of my foot, and it didn't go away. It only kept getting worse," he said. "I have never had anything like this before, ever."
MASTER FEDERER
Even before the injury slowed the seventh-seeded American, Federer was the master, tempering Isner's big serves and winning 32 of 35 points on his own serve
"Roger was too good," Isner said. "In the first five games, I was fine. Nothing was bothering me. He was all over me."
Federer elected to receive to open the match and the strategy paid off as he broke Isner.
The American held on the third game but Federer took the next four.
Isner played much better in the second set but in the end the pain became too much, even with a medical examination after the seventh game.
"I knew at 3-4, whatever, I knew I wasn't going to win. I can tell you that much," said Isner.
"Which is a weird feeling, you know, being on serve in the finals of a match and knowing that I wasn't going to win."
Federer also sensed the American was in trouble.
"I knew it was going to be something that was not right. The way he was moving was not well," Federer said.
"But at the same time I have got to make him work hard, keep doing my things."
The title was Federer's second of the year, coming after his historic 100th win in Doha in February.
(Reporting by Gene Cherry in Raleigh, North Carolina, editing by Pritha Sarkar and Ken Ferris)
