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.
Victory was overshadowed though by fresh speculation in the Spanish media linking winger Cristiano Ronaldo with a move to Real Madrid, reports angrily denied by manager Alex Ferguson.
"Do you think I would get into a contract with them?", Ferguson told reporters. "They've got no chance. There's no agreement whatsoever between the clubs.
"I wouldn't sell them a virus. It can be an angry situation and annoying but we know their game. The best thing for us is to ignore it."
Wayne Rooney netted twice moments after coming on as a substitute, his first goal arriving 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 headers by Nemanja Vidic and Ronaldo had given United a 2-0 halftime lead.
"The fans got their money's worth," added Ferguson. "I don't know what the score could have been. Edwin van der Sar made three tremendous saves to secure the win for us."
Yasuhito Endo pulled back a goal from the penalty spot for Gamba before Hideo Hashimoto smashed his side's third in injury time, the sixth goal in 17 crazy second-half minutes.
IRREPRESSIBLE ROONEY
Ronaldo, wearing lime green boots, mesmerised the crowd of 67,000 with some dazzling stepovers but it was the irrepressible Rooney who stole the show.
The England striker made an immediate impact after coming on, producing a clinical left-foot finish with his first touch.
Rooney then latched on to an excellent through ball from Ryan Giggs to sweep home his second.
With the latest row between United and Real threatening to erupt, Ronaldo chose his words carefully.
"I don't care, I don't read the newspapers," he shrugged. "We're out here in Japan and I don't know anything about what's happening around me. I'm very happy at Man United."
Ferguson's side won the tournament's forerunner, a one-off match between the champions of Europe and South America, with a 1-0 victory over Brazil's Palmeiras in 1999.
United were beaten 2-1 on aggregate by Argentines 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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