Both men had previously been sanctioned for an incident in the corresponding fixture last season when Madrid boss Mourinho poked a finger in the eye of Vilanova, who is now the new Barca head coach after he moved up to the role having previously been Pep Guardiola's assistant.
Mourinho was handed a two-game ban and Vilanova one for his retaliatory slap.
The suspensions were applicable only in Supercopa games, but have now been lifted as part of an amnesty by the Spanish Football Federation (RFEF).
"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 organisation's general assembly in Madrid on Tuesday.
Barca reacted with disappointment to the news.
Club president Sandro Rosell insisted last month the club would oppose the lifting of any punishment against Mourinho and board spokesman Toni Freixa said on Tuesday it was a "very bad example for football".
Freixa added: "Yesterday [Monday] President Rosell, in front of the board of directors of the Federation, expressed our disagreement with the measure.
"He suggested that the suspension was the only effective measure as aggression can never go unpunished."
The first leg of the Supercopa, the season curtain-raiser between the Primera Division winners (Madrid) and Copa del Rey champions (Barcelona), takes place at the Nou Camp on August 23 with the return at the Bernabeu a week later.