With more than a month to go until the start of the 2012/13 La Liga campaign, bad blood has already boiled up between the bitter rivals.
Barca spokesman Toni Freixa said Mourinho's exoneration, part of a general amnesty for sanctioned players and coaches, damaged the image of Spanish football and would only encourage further aggression.
The volatile Portuguese was punished after attacking Vilanova, who has since taken over as first-team coach from Pep Guardiola, from behind during a Super Cup match.
However, the ban was rescinded by football federation (RFEF) president Angel Maria Villar, who traditionally exonerates some players and coaches after sealing re-election.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 and his latest amnesty was announced at the RFEF's general assembly in Madrid earlier on Tuesday.
Freixa said Barca president Sandro Rosell had expressed the club's displeasure at the prospect of Mourinho's ban being lifted at a federation board meeting on Monday.
"As we understand it, an aggression towards a coach deserves punishment," Freixa said on Barca's website.
"This decision does not mean the aggressor is innocent, but leads them to believe that they can continue to attack people without fear of punishment," he added.
"It's a bad example for Spanish football that this aggression is going unpunished."
PROTAGONIST BARCA
The federation's decision meant Vilanova's one-match ban for reacting to the aggression was also lifted, as were bans given to Real pair Mesut Ozil and Marcelo and Barca's David Villa, who were all red-carded during the match.
All five are now clear to take part 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.
Real director Emilio Butragueno said Barca had benefited from Villar's amnesties in the past without Real commenting or taking any action.
"The federation president has the power to do it and we are respectful of that," the former Real and Spain striker said on Real's website.
"We won't mention things that are in the past, but everyone is familiar with them and Barca was the protagonist and Madrid never said anything," he added.
One player who did not benefit from Villar's generosity was Granada's Dani Benitez, who was banned for three months after throwing a plastic bottle at the referee after his side lost to Real last season.
"I wasn't expecting to have my ban lifted," Benitez was quoted as saying by Marca sports daily.
"In Spain the big teams have always had an advantage compared to the small ones," he added.
"What I did was more serious than Mourinho's but Mourinho's is also serious."
The first leg of this year's Super Cup is at Barca's Nou Camp stadium on August 23, with the return leg at Real's Bernabeu arena
