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Malaga had the first opportunity on goal after six minutes, but Ignacio Camacho could not hit the target with his header.
After nine minutes, Valladolid took the lead thanks to a goal from Manucho Goncalves.
The away side threatened again, but Patrick Ebert's shot was well saved by the goalkeeper.
Malaga began to push forward much more and had a chance after 18 minutes, though Francisco Portillo Soler could not find the finish needed.
After 37 minutes, Malaga finally found the equaliser and it was Isco who made it 1-1.
Three minutes after the restart, Manucho had a chance to put Valladolid back in front, but his effort was denied by the goalkeeper.
Isco had a chance to grab his second of the game after 62 minutes, but his chance was squandered.
Malaga were given a golden opportunity to take all three points when the referee awarded them a penalty after 84 minutes for a foul by Henrique Sereno.
Joaquin stepped up for Malaga but missed the spot kick, leaving the scores level.
The home side continued to drive forward in search of a late winner and soon found one after 87 minutes. Joaquin made it 2-1 to make up for his penalty miss two minutes earlier.