United substitute Wayne Rooney scored twice moments after coming on, getting his first goal seconds after Gamba striker Masato Yamazaki had pegged the score back to 2-1 in the 74th minute.
Darren Fletcher also got on the scoresheet after coming off the bench as the game exploded into life after Nemanja Vidic and Cristiano Ronaldo headers had given United a 2-0 halftime lead.
"The fans got their money's worth," United manager Alex Ferguson told reporters. "I don't know what the score could have been. Edwin van der Sar's made three tremendous saves."
Ferguson angrily rejected the latest speculation linking Ronaldo with a move to Real Madrid, with Spanish media reporting that there was an agreement between the clubs.
"They've got no chance. There's no agreement whatsoever between the clubs," Ferguson said.
European champions United, heavy favourites to become the first British team to win the seven-team FIFA tournament, will face Ecuador's LDU in Sunday's final in Yokohama.
Yasuhito Endo pulled back a goal from the penalty spot for J-League side Gamba before Hideo Hashimoto smashed his side's third, the sixth goal in 17 crazy second-half minutes.
Ronaldo, resplendent in a pair of lime green boots, mesmerised the crowd of 67,000 with some dazzling stepovers but was overshadowed by Rooney.
IMMEDIATE IMPACT
The England striker made an immediate impact on the match after coming on, producing a clinical left-foot finish with his first touch.
Rooney's second followed Fletcher's neat near-post header when he latched on to an excellent through ball from Ryan Giggs to sweep home five minutes later.
"It was brilliant out there -- a great atmosphere," said Ronaldo. "We didn't play that well in the second half but we'll be better in the final. We'll be ready for that."
Ferguson's side won the tournament's forerunner, a one-off match between the champions of Europe and South America, with a 1-0 win over Brazil's Palmeiras in 1999.
United were beaten 2-1 on aggregate by Argentine side Estudiantes in 1968 when the Intercontinental Cup was played over two legs.
Gamba manager Akira Nishino paid tribute to his players.
"We gave them two easy goals from corners and that killed us," he said. "We weren't given a prayer to win this game but we scored three goals so we have to be proud."
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