Nalbandian went into the final with a 6-5 career record against Federer
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World number one Roger Federer reached his first French Open final when David Nalbandian pulled out of their semi-final with a stomach injury.
Federer had made a poor start and trailed by a set and a break before finding his best form to fight back.
With the match in the balance early in the third set Nalbandian called for the trainer, and four games later, at 3-6 6-4 5-2 down, he conceded defeat.
Federer will play Rafael Nadal, who beat Ivan Ljubicic, in Sunday's final.
"It's very tough, we were playing well, we were fighting," said Federer after outlasting Nalbandian.
"I really thought I was going to lose that match. I was fortunate, I was not doing too well."
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David played a great first set and a half but then I started to hit some fabulous shot
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Nalbandian explained: "All of a sudden, I felt a very sharp pain that was worse than during the previous match.
"I've had this injury two or three times already. You feel very bitter about it. You feel very bitter having to retire like that."
A shock had looked possible in the early stages as Federer began nervously and struggled in the wind, making numerous unforced errors.
A calm Nalbandian broke Federer for the first time in game five and again to take the set in game nine, to the delight of a large Argentine contingent on Phillipe Chatrier Court.
And when he quickly moved 3-0 clear in the second set, the much-anticipated Federer-Nadal final looked like being put on hold for another year.
But Federer found inspiration from an improvised forehand-slice winner to break back, and two games later he chased down a lob to fire a spectacular winner down the line with his back to the net.
"You can't pull those off on a consistent basis but they give you a bit of tailwind, something extra," he admitted afterwards.
Nalbandian was understandably rocked by the sudden onslaught as Federer reeled off 11 of the next 14 games.
The third seed called for the trainer and the doctor midway through the third set for a stomach injury - something he suffered with earlier in the year.
And when Federer went a double break up and closed on a two-sets-to-one lead, the Argentine knew the game was up.
"David played a great first set and a half," said Federer. "But then I started to hit some fabulous shots, and it gave me confidence."