But Barca failed to fire before Gerard Pique's shot set up a frantic finale.
Banega had put sixth-placed Valencia ahead in the 33rd minute after a failed clearance by Gerard Pique.
Barcelona's central defender Gerard Pique had tweeted Saturday that he wanted politics to say out of El Clasico.
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Gerard Pique's shot deflected in off Yaroslav Rakitskiy but Rakitskiy turned a cross in as Shakhtar pulled one back.
Songs by pop star Shakira are banned at the ground of Real Madrid because her boyfriend Gerard Pique plays for rivals Barcelona.
He left out stalwart defender Gerard Pique for the fourth straight game as well as Alexis Sanchez and Cesc Fabregas, his two biggest summer signings.
On 55 minutes Andres Iniesta side-footed home from 12 yards before a Steven Naismith diving header and a Gerard Pique own-goal levelled the tie.
Real got off to the perfect start when their star striker Cristiano Ronaldo won a penalty after a challenge from Gerard Pique on 13 minutes.
Gerard Pique's header was cleared off the line by Young, but when Rio Ferdinand reacted first, Gardner could only lash his attempted clearance into his own net.
However, Barca regrouped after the break and levelled just seven minutes into the second period, when Swedish striker Ibrahimovic was on hand to finish from Gerard Pique's nod down.
But when Gerard Pique saw red immediately after the break, the visitors were handed a lifeline which they duly grabbed -- David Barrel leveling the scores in the 49th minute.
His side were unable to formulate an alternative to their usual fluent style until the stand-in coach chose to use defender Gerard Pique in a makeshift attacking role for the final minutes.
Reports on the Spanish website El Confidencial, claimed Metodo 3 trailed defender Gerard Pique and his pop star wife Shakira in 2010 -- following them to a concert to log their activities.
There was little doubt that Gerard Pique fouled Cardozo for the first when he clung onto the Benfica forward, but the Paraguayan's subsequent penalty was struck at a good height for Casillas.
Colombian pop star Shakira hung out in Ginza with defender Gerard Pique, while Cesc Fabregas shopped for electronic gadgets in Akihabara and soft-spoken midfielder Andres Iniesta was spotted on the Tokyo subway.
David Villa and substitute Cristian Tello scored in the second half before Getafe hit back through striker Alvaro Vazquez, but then Andres Iniesta and defender Gerard Pique netted in time added on.
But Felipe Caicedo pounced on a defensive error to equalize four minutes before halftime, slotting into the empty net after Gerard Pique missed his attempted clearance to leave goalkeeper Victor Valdes stranded.
The Catalan side, playing in its sixth successive semifinal, appeared rattled by Bayern's approach and was fortunate not concede a penalty when Gerard Pique clearly handled Philipp Lahm's strike inside the penalty area.
The game was only two minutes old when Barcelona keeper Victor Valdes fumbled Ronaldo's free-kick, and only the crucial intervention of former United defender Gerard Pique prevented Ji-Sung Park turning in the rebound.
Among his peers were current Barcelona centre-back Gerard Pique and a certain Lionel Messi, who was signed from Newell's Old Boys in Argentina as a 13-year-old and played with Fabregas for Borrell's under-14s.
Although far from its fluent best, Barcelona picked up in the second half and Gerard Pique netted four minutes after the interval only for Roque Santa Cruz to pull Malaga level once again.
Gabi dispossessed Gerard Pique and fed the ball to striker Radamel Falcao, who netted his 28th goal this season to stay third in the "Pichichi" scoring stakes behind Messi (46) and Cristiano Ronaldo (34).
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.
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.
"I congratulate Real Madrid for their victory and also for their league title which I have no doubt they have clinched tonight, " Guardiola told reporters, as he defended his decision to leave Cesc Fabregas and Gerard Pique on the bench.
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He made a rash charge from his goal as Ibrahimovic went in chase of Gerard Pique's long ball, leaving the striker with the easy option of lofting the ball over the onrushing Almunia to give the visitors the lead they thoroughly merited.
Gerard Pique over-hit a long pass out of defence - which the out-of-sorts Torres was never likely to reach - but Chile goalkeeper and captain Claudio Bravo foolishly raced out of his penalty area to clear unsuccessfully into the path of Villa.
If you buy the first argument that they still count as homegrown because the year or two they spent with the youth teams was sufficiently formative then you have a problem when it comes to two other La Masia products in defender Gerard Pique and midfielder Cesc Fabregas.
Playing with a big cushion after a 4-0 win in the first leg at home last week, Bayern beat Barcelona 3-0 in the second leg Wednesday night on goals by Arjen Robben in the 48th minute and Thomas Mueller in the 76th around Gerard Pique's own goal in the 72nd.
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