The Spain international was dismissed around the hour mark following a verbal tirade at a linesman over the absence of an offside flag against Aritz Aduriz.
Referee Velasco Carballo claimed in his post-match report that Pique shouted "I s*** on your w**** mother" at his assistant, an indiscretion for which the centre-back could have been banned between four and 12 games.
The 28-year-old came out on Tuesday to apologise for his behaviour, although he insisted he didn't utter any of the words mentioned in the referee's report.
Barcelona also stood by their man, publicly declaring his innocence.
But the RFEF was not impressed by the Catalans' protests though and has decided to hand the defender a four-game ban.
Pique will consequently miss the Liga encounters with Athletic Bilbao, Malaga, Atletico Madrid and Levante.
He could return to match action in the away game to Celta de Vigo on September 23.
Pique's absence leaves Luis Enrique short of options in defence, with Thomas Vermaelen, Jeremy Mathieu, Marc Bartra and Javier Mascherano as his only remaining alternatives at centre-back.