Ramires tumbled under challenge from Evra while Torres went down as he tangled with Antonio Valencia.
Portugal had led 2-1 after Ronaldo and Helder Postiga had overturned Antonio Valencia's second minute strike.
Dutchman Van Persie then connected with an Antonio Valencia cross to make it 2-0.
But instead he becomes United's second summer signing after the recent addition of Antonio Valencia from Wigan.
Elsewhere, Ecuador beat Bolivia 3-1 with goals from Edison Mendez, Manchester United's Antonio Valencia and Birmingham's Cristian Benitez.
However, it was winger Antonio Valencia's first-half miss that irked Ferguson the most.
United put on a superb display at Old Trafford, with former Wigan winger Antonio Valencia impressive against his former club.
United have brought in Michael Owen, Antonio Valencia and Bordeaux's Gabriel Obertan to replace departed forwards Cristiano Ronaldo and Carlos Tevez.
United leveled on the half hour mark when Japan international Shinji Kagawa teed up Antonio Valencia to slot home from close range.
The lively Caleb Folan then blazed over the bar following good work by Antonio Valencia and Heskey also had a shot blocked.
Ji-Sung Park hit the post for United before Rooney rose to head the outstanding Antonio Valencia's cross past Friedel with 16 minutes left.
Paul Robinson made an excellent save after Antonio Valencia had been played clean through and later held a shot from an unmarked Dimitar Berbatov.
Antonio Valencia rounded off a terrific display with a fine chipped fifth and, in truth, it could have been more as relegation candidates Wigan crumbled.
Nine minutes from time United's Antonio Valencia seized a wayward Liverpool pass, raced through on the Liverpool goal and was brought down by Glen Johnson.
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After losing Emile Heskey and Wilson Palacios in January, it seems likely that Antonio Valencia will follow them out of the JJB Stadium this summer.
Ferguson insisted players such as Hernandez, Darron Gibson, Antonio Valencia and Ji-Sung Park should have been good enough to carve out opportunities against the Scottish champions.
Rooney exchanged passes with Antonio Valencia as the pair led a swift United counter-attack before the England striker won a penalty after being fouled by Brown.
Manchester United took the lead at Arsenal's Emirates Stadium in north London when Antonio Valencia headed home Ryan Giggs' cross on the stroke of half time.
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United have been linked with moves to sign Bayern Munich's France star Franck Ribery and Wigan's Ecuador winger Antonio Valencia as Ferguson seeks to replace Ronaldo.
Not that United's backline needed to be at its strongest, with Pompey chasing shadows for much of the game as Nani, Antonio Valencia and Rooney ran riot.
Antonio Valencia escaped from Leighton Baines and when his cross caused confusion in the Everton defence, Berbatov pounced to power home a finish via the underside of the bar.
The Old Trafford faithful were barely vocal in the opening half an hour with neither team doing little to threaten a goal, apart from a mistimed volley from Antonio Valencia.
Rooney's deft header played in Antonio Valencia but the winger lacked the incisiveness to get a shot away, while Michael Carrick's shot from 20 yards brought a decent save from Friedel.
On an afternoon when England's World Cup flops were booed by the vast majority of the 84, 623 inside Wembley, Wayne Rooney played a superb low pass for Antonio Valencia's opening goal.
Last season, Manchester United's Luis Antonio Valencia missed seven months with a broken leg, before returning deep into March with the club three points clear at the top of the table.
Brazilian midfielder Anderson crossed for Antonio Valencia to score the third from close range 10 minutes later, and the Ecuador winger set up England striker Wayne Rooney just 60 seconds after that.
Having surrendered a first-half goal to Manchester United's Antonio Valencia, Arsenal regrouped at halftime and eventually tied the game up in the second half, thanks largely to the promising play of teenage winger Alex Oxlade-Chamberlain.
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Nani came on for Jones and twice went close, volleying narrowly wide before forcing Federici to tip over his fierce shot but the pressure finally told as the Portuguese tucked home from Antonio Valencia's cross.
Matching up against Chelsea's diamond formation, with Rooney floating and Antonio Valencia pushed up against left back Ashley Cole, United stifled their opponents' rhythm and just had the better of a keenly fought first half.
Scharner had a shot blocked while Cech, playing with a special chin strap to protect the 50 stitches he had in a facial wound last week, made a smart save at his near post to deny Antonio Valencia.
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