Xabi Alonso turned a cross into his own net after just ten minutes and when Iker Casillas failed to deal with Ivica Dragutinovic's free kick Sevilla were on course for a famous win.
But Cristinao Ronaldo swept home a cross on the hour to give Real hope before Sergio Ramos brought the home side level just four minutes later.
Just seconds remained when Van der Vaart capitalised on a loose ball after Andres Palop had saved from Gonzalo Higuain to seal a thrilling victory.
Carles Puyol lies stricken after his own goal against Almeria
Barcelona twice came from behind to claim a point at Almeria in a match that finished 2-2.
Domingo Cisma had put Almeria ahead after 12 minutes, with the home side's second coming 12 minutes into the second period via a Carles Puyol own-goal.
But either side of those home goals, Lionel Messi scored a sublime free kick and then a close range tap in to save ten-man Barca a point.