Iker Casillas saved brilliantly from Giggs, but United's master marksman was on hand to score.
Hamit Altintop brought down Adorno for a penalty and Estbeban Solari sent Iker Casillas the wrong way.
Spain goalkeeper Iker Casillas and Brazil custodian Julio Cesar have previously suggested the ball is difficult to control.
Elsewhere, Iker Munian's late goal handed Athletic Bilbao a much-needed victory over Valencia while Levante and Getafe drew 0-0.
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Lyon could have been further in front, with a volley from Cesar Delgado coming back off Iker Casilla's right post.
For Real Madrid and Spain goalkeeper Iker Casillas, they have even become the norm, so Neuer is in good company.
Spain's Iker Casillas was awarded the Golden Glove prize for the best goalkeeper after conceding just two goals in the tournament.
The World and European champions rarely threatened and were indebted to goalkeeper Iker Casillas for keeping them level on the hour mark.
Despite Mourinho's apparent dressing room rift with former captain Iker Casillas and other key Spanish players, Real defender Alvaro Arbeloa said the 50-year-old deserved respect.
And the home side nearly doubled their advantage just seven minutes later when Domingo Cisma's free-kick was superbly saved by Iker Casillas.
England's David James, Italy's Gianluigi Buffon and Iker Casillas of Spain were among the goalkeepers who criticised the Jabulani before the tournament began.
Valencia improved after the break and tested Real goalkeeper Iker Casillas -- recently dropped by Mourinho -- several times but Real held firm.
Just before the hour mark, Ronaldinho skipped past two challenges before racing into the box and firing the second past the helpless Iker Casillas.
Fernando Torres was the first to race through on goal but his angled shot from the right was excellently palmed wide by Iker Casillas.
Cruyff described Real's start to the season as a "failure", while also questioning coach Jose Mourinho's decision to drop Spanish international goalkeeper Iker Casillas.
On Saturday Madrid twice came from behind, but goalkeeper Iker Casillas' error in stoppage time gifted Villarreal the victory that ended any lingering title hopes.
Joao Moutinho, the first Portuguese player up, saw his shot saved by Iker Casillas, and defender Bruno Alves clanked the fourth kick against the crossbar.
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In the second half, Messi was fouled just outside the Real penalty area and got up to send an unstoppable free kick past Iker Casillas.
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Having fallen out with Real Madrid fan favorite Iker Casillas, Mourinho drew criticism from his fellow Portuguese, defender Pepe, who said Mourinho should have shown Casillas more respect.
Spanish captain and goalkeeper Iker Casillas saved penalties by Daniele de Rossi and Antonio Di Natale to leave Cesc Fabregas to beat Gianluigi Buffon with the deciding kick.
And things got worse as keeper Iker Casillas failed to handle a long throw just before halftime and Pablo Garcia lobbed the loose ball over him into the net.
Style of play which has frustrated supporters, a falling out club captain Iker Casillas and a constant war of words with the Spanish media has not helped his case.
Undaunted, the ever-threatening Beausejour raced away from Spain's back-line as he nearly created a dangerous one-on-one with keeper Iker Casillas - but Pique sped back to make a crucial block.
But his performances have yet to convince Spain manager Luis Aragones, who has a plethora of world-class goalkeepers at his disposal, including Real Madrid's Iker Casillas, Valencia's Santiago Canizares and Liverpool's Pepe Reina.
Mourinho confirmed that his captain and experienced goalkeeper Iker Casillas would not be returning despite traveling with the team and training Tuesday at the Etihad Stadium, home of United's great rivals Manchester City.
Madrid twice came from behind to draw level, but goalkeeper Iker Casillas' error in stoppage time gifted Villarreal the victory which leaves Juande Ramos' side eight points behind Barca with just two games left.
Twice Cristiano Ronaldo tried his luck from long range with free-kicks, and on the second occasion Spanish goalkeeper Iker Casillas could not hold on to the ball and Gerard Pique had to mop up.
It was heartbreaking for a Paraguay side that had never reached the quarter-final stage before, and who earlier wasted a superb chance to take the lead when Oscar Cardozo's spot-kick was saved by Iker Casillas.
The striker, who was surprisingly brought on for South Africa's best player, midfielder Steven Pienaar, controlled a left-wing cross by Siphiwe Tshabalala with his knee and stabbed the ball past Iker Casillas in the 73rd minute.
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