Substitute Rooney came on to score his eight and ninth goals of the season
Manchester United eased through to the Fifa Club World Cup final despite a spirited late effort from Gamba Osaka.
Nemanja Vidic and Cristiano Ronaldo easily converted first-half headers but Masato Yamazaki pulled a classy goal back for the plucky Japanese side.
Substitute Wayne Rooney bustled through to score with his first touch seconds later before Darren Fletcher nodded in.
Dangerous Rooney added a fifth though a late flurry saw Yasuhito Endo convert a penalty and Hideo Hashimoto fire home.
Sir Alex Ferguson's side now face Ecuador's Liga de Quito in Sunday's final, while Osaka will meet Mexico's Pachuca in the match for third place.
Critics have questioned the credibility of a tournament where the gap in the teams' abilities may on paper appear vast, but a thrilling end to this match - with six goals in the last 16 minutes - will at least arm Fifa with some positive ammunition.
Ferguson, though, insists his Champions League holders are keen to become the first British side to win it and showed that with a strong starting line-up, though Dimitar Berbatov was absent through illness and Rooney started on the bench - before appearing to such effect.
"I think Wayne can be a number nine," said Ferguson after the match. "We are trying to develop him that way.
"We have tried to play him there for most of the season. His movement, strength and penetration are very good."
Reigning Asian Champions League winners Gamba gave as good as they got in a lively start in Yokohama, getting the vocal crowd right behind them and not looking like a side who had lost four of their past five games.
Tomokazu Myojin hit a decent long-range shot to test United keeper Edwin Van der Sar before Carlos Tevez raced down the other end to put in an enticing cross for Ryan Giggs.
Van der Sar then had to make a smart block when one-on-one with Ryuji Bando after 13 minutes, but United began to show the greater synergy from that point on.
Ronaldo saw much of the ball and his typical tricks on edge of the box, drawing four defenders out of position, enabled him to fire just wide of the upright.
United took a deserved lead in the simplest fashion on 27 minutes when Giggs floated over a corner and Vidic - who later went off with a slight groin strain - rose higher than skipper Yamaguchi to nod in while keeper Fujigaya flapped at thin air.
Unmarked Anderson should have then grabbed his first goal for United but could not get a firm connection on Ronaldo's cross.
With Gamba largely consigned to off-target long-range efforts, Ronaldo put United two ahead with another uncontested header from a decent Giggs corner in first-half injury time.
Evra slipped Tevez clear of Gamba's defence just after the break but referee Benito Archundia Tellez blew his whistle for offside before the Argentine slipped past the keeper and knocked the ball into an unguarded goal.
With the match drifting into exhibition mode, it took an explosive turn with the 73rd minute substitution of Tevez for Rooney.
Ronaldo and Vidic both converted simple first-half headers
As soon as the Liverpudlian trotted on Gamba had the ball in the net, Masato Yamazaki superbly slotting home from 16 yards after he was found in space in the penalty area.
Yet, with the next attack, Darren Fletcher drifted a through ball over the top for fellow substitute Rooney who, after failing to control the ball on his chest, pounced to scramble a left-footed shot across the body of Fujigaya.
Minutes later Fletcher headed in smartly himself after Patrice Evra whipped in a dangerous cross from the left wing.
And the rapid goal rush continued when Rooney grabbed his second in the 78th minute, the England striker instinctively toe-poking the ball low into the goal after great build-up play from Nani then Giggs.
"For the third goal that really killed them he made two runs, across and back and across and behind," added Ferguson. "They were really clever.
"It marks out the quality he can give you in that position and he will improve from there."
But with the Premier League champions cruising at 5-1 up, captain Gary Neville was adjudged to have handballed Bando's cross and Endo calmly slotted in an excellent penalty.
Gamba then lifted the atmosphere to new to hit an unlikely third as Hashimoto lashed the ball into the top corner from the edge of the area with Van der Sar brilliantly beaten.
Man Utd: Van der Sar, Neville, Ferdinand, Vidic (Evans 69), Evra, Nani, Anderson, Scholes (Fletcher 67), Ronaldo, Giggs, Tevez (Rooney 73). Subs Not Used: Kuszczak, Rafael Da Silva, O'Shea, Carrick, Gibson, Park, Welbeck, Amos.
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