The decision, announced at the RFEF's general assembly in Madrid, raises the prospect of a clash between the federation and Barca, whose president Sandro Rosell said last month he would not allow Mourinho's aggression to go unpunished.
The volatile Portuguese was sanctioned after attacking Vilanova, who has since taken over as first-team coach from Pep Guardiola, from behind during a Super Cup match last season.
The ban, applicable only in the Super Cup, was rescinded by RFEF president Angel Maria Villar, who traditionally exonerates some players and coaches after sealing re-election. He was voted in unopposed for a seventh four-year term in February.
"Match bans up to four games and stadium bans up to two games will not be enforced," the RFEF ruled, according to a note distributed at the assembly.
The ruling meant Vilanova's one-match ban for reacting to Mourinho's aggression was also lifted.
Both can take their place on the bench when La Liga champions Real and King's Cup winners Barca meet next month in the 2012 Super Cup, the two-legged curtain-raiser to the season.
Rosell suggested last month the club would challenge any decision to exonerate Mourinho.
"We do not accept that an aggression towards our coach is not punished," Rosell said.
"If this happens, we will speak to the appropriate party, we will not let it go unpunished."
