Puyol was sent off and the Arsenal skipper completed the formalities from the spot.
The only downside was the early departure of Carlos Puyol, who limped off in the 57th minute.
The move comes after teammates Carles Puyol and Xavi Hernandez both signed new deals with the club.
Barcelona players Carlos Puyol and Xavi retain their places after dropping out of the Iceland game because of injury.
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His replacement Carles Puyol picked up a yellow card, which means he will be suspended for the return leg.
If you're going to count them as La Masia products, you can't really count Pedro, Puyol and Busquets, as well.
Spain defender Joan Capdevila wasted a good chance shortly after the restart, failing to make contact with a Carles Puyol flick-on.
The lead didn't last long though with Carlos Puyol scoring in the 36th minute and Messi adding a second three minutes later.
With Puyol's later red card also ruling the Barca skipper out, Barcelona will be without both first-choice centre-backs at the Nou Camp.
Pedro is often referred to as a La Masia product, but he joined at 17, as did Puyol and defensive midfielder Sergio Busquets.
Robben's pace troubled the Spanish defence throughout and another burst from the Bayern Munich man unsettled Puyol, who appeared to impinge his opponent.
Puyol was sent off and misses next week's second leg, as will Fabregas after he picked up a yellow card in the first half.
But Barca, which has not lost a domestic game this season, hit back through Lionel Messi and Carles Puyol to lead 2-1 at the interval.
Late in normal time Robben was also through and appeared to be pulled back by Spain defender Carles Puyol before Casillas saved again at his feet.
Barcelona also was missing defenders Carles Puyol and Javier Mascherano and midfielder Sergio Busquets because of injuries, and left back Jordi Alba because of a suspension for yellow-card accumulation.
Suddenly, however, the momentum was with Wenger's men and, with five minutes left, they were level after Puyol bundled over Fabregas as he prepared to shoot in the area.
While both club captain Puyol, 34, and Xavi, 32, are significant figures at the club, Barcelona officials are likely to look upon the extension of Messi's deal as the most important.
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Ronaldo, for all his obvious frustrations that ended almost inevitably in a yellow card for a late barge on Carles Puyol, never stopped running but this was not to be his night or United's.
Spain will have to weather the game's most competitive tournament without the country's all-time leading scorer, David Villa, who is recovering from a broken leg, and top defender Carles Puyol, who just had knee surgery.
Barca coach Pep Guardiola is missing suspended captain Carles Puyol and fellow defender Gerard Pique, while Dmytro Chygrynskiy is cup-tied, so Mexico international Rafael Marquez and Argentina's Gabriel Milito should feature in the back four.
Seven of the 11 players who beat Manchester United in last season's Champions League final came through La Masia, and if an injury hadn't cost Carles Puyol his starting spot, that number would have been eight.
"Here is where the stars all started, " added Folguera, throwing a proud glance at photographs of some of the most illustrious years to have graduated from La Masia: one includes Liverpool goalkeeper Pepe Reina with Xavi and Puyol.
That should have acted as a warning for Spain, but they were caught on the break again early in the second half and were lucky to escape when Almeida's cross span off Carlos Puyol and looped just beyond the far post.
He raced clear to fire under Valdes with 21 minutes left - and Cesc Fabregas turned logic on its head, given the evidence of the previous 85 minutes, by scoring from the spot after he was brought down by Barcelona captain Carles Puyol.
Almeria went ahead for a second time in the game when Puyol put through his own net in the 57th after he diverted a cross from Brazilian Guilherme past Valdes before Ibrahimovic was sent off on the hour mark for a needless foul on Cisma.
Van der Sar saved well from Puyol as Barcelona dominated until the final whistle - and not even the most partisan Manchester United follower can doubt that Pep Guardiola deserved to round off a dream first season in charge by adding the Champions League to the La Liga title and the Spanish Cup.
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