Pep Guardiola's former assistant, who has since stepped up to the top job, was deliberately poked in the eye by Real Madrid boss Mourinho during a melee on the touchline at the end of last season's Spanish Super Cup between the sides.
"What happened in that game, that is still being talked about a year further on, I am tired of it," Vilanova told a news conference.
The Spanish federation (RFEF) imposed a two-match Super Cup ban on Mourinho, and one on Vilanova for reacting to the aggression by pushing him away.
Last week, newly re-instated federation president Angel Maria Villar lifted the punishments as part of a general amnesty, something he has traditionally done to players and coaches after sealing re-election.
The ruling prompted an angry reaction from Barcelona with club spokesman Toni Freixa saying Mourinho's actions could not be allowed to go unpunished.
"The one-man panel imposed a sanction, the president decided on an amnesty (for us), and I accept it. It has worked this way for many years," Vilanova added.
"The biggest punishment the two of us will have are the images, that people will be able to see for many years."
Vilanova was giving his first news conference since the club returned to start pre-season training on Monday and inevitably he was asked if there was any lingering bad blood between him and the coach of their arch-rivals, the La Liga champions.
"Mourinho has already greeted me at the Bernabeu in the league (since then), and I don't think we have a bad relationship," he said.
Barcelona resume their rivalry with Real Madrid in the Spanish Super Cup, the traditional curtain-raiser to the new season between the league champions and the Copa del Rey winners next month.
The first leg is at the Nou Camp on Aug. 23, with the return at the Bernabeu on Aug. 29.