The Spaniard had already served a one-match suspension after being sent off for two bookable offences during the Carling Cup tie in August.
But the 31-year-old was charged with improper conduct for failing to leave the field promptly after his dismissal and throwing a water bottle to the ground in front of the linesman.
A Swansea spokesperson said: "We put forward a very good case and the FAW gave us a fair hearing.
"Our case must have been very strong because charges relating to improper conduct normally carry a two-match ban and a hefty fine."
Pintado will will miss the visit of QPR on October 3.