Malaga sanctioned after Valencia protests
Weligton and Apono were given two-match bans after referee Antonio Rubinos Perez said he and his fellow officials were verbally abused as they made their way to the changing rooms after the game.
Apono's suspension extends to three games as he also collected a fifth yellow card.
Malaga will also go into Saturday's home match against Real Zaragoza without Chilean coach Manuel Pellegrini, who was sent from the dugout for protesting eight minutes from time at Mestalla.
The south-coast club took an early lead against Valencia before losing Argentina defender Martin Demichelis to a straight red card. Helder Rosario was later sent off.
Demichelis is also suspended for Saturday's match but the RFEF rescinded Rosario's red card, which was given for making a rude gesture at a linesman.