Sevilla stunned the home fans by taking a two-goal at the Bernabeu with an own-goal from Xabi Alonso and an Ivica Dragutinovic free-kick early in the second half.
Real stormed back, netting twice in four minutes through Cristiano Ronaldo and Sergio Ramos and the winner came when Van der Vaart scrambled the ball home in added time.
Sevilla spoiled a festive atmosphere at the Bernabeu, following the news of Barca's draw in Almeria, by grabbing an early goal when Diego Capel's cross was turned into his own net by Alonso in the 10th minute.
Dragutinovic's speculative long-range free-kick looked harmless but goalkeeper Iker Casillas was unsighted and the ball bounced inside the post.
Gonzalo Higuain hit the post and the bar, Raul got in the way of Ronaldo's goal-bound shot and Sevilla barely emerged from their own half.
Almeria keeper Diego Alves was in fine form and as Barca's frustrations grew, coach Pep Guardiola was sent to the stands for disputing a decision.
Alves held firm until just before half time when Barca won a fortunate free-kick on the edge of the area and the keeper could only watch as Messi's superb effort curled into the top corner.
Almeria were back in front after the break when Carles Puyol turned Guilherme's low cross into his own net.
Four minutes later Barcelona's Sweden striker Ibrahimovic was sent off when Cisma made the most of a tussle between the two.
