The Liga side took the lead through Tiko (42), however minnows Gimnastica overturned the scoreline with goals from Javi Delgado (68) and Javi in injury time.
Real Madrid swept past lowly San Sebastian de los Reyes with goals from Raul (29), (57) and Esteban Cambiasso (88).
David Beckham was rested for the game, as were first team regulars Ivan Helguera, Michel Salgado, Zinedine Zidane and Ronaldo.
Deportivo La Coruna squeezed past Second Division Compostela, courtesy of a Diego Tristan goal in the 82nd minute.
Valencia's game at Castellon was suspended nine minutes from time - with the score at 1-1 - when referee Tellez Sanchez was struck by a missile from the crowd after awarding the visitors a penalty.
Castellon had taken the lead on 39 minutes through Marcos, the first goal Valencia had conceded for some 642 minutes in all competitions.
However, Ruben Baraja hit back with an equaliser on 63 minutes before the match official opted to call proceedings to a halt.
A late Ronaldinho (pictured) goal (84) saw Barcelona through against Catalan side Gramanet.
Villarreal narrowly beat Alicante 2-1. Juan Roman Riquelme opened the scoring on 61 minutes with Alicante equalising on 79 through Sendoa.
Former Real Madrid midfielder Victor sealed the win for the Liga side with an injury time penalty.
