The Argentina forward, a favourite to secure a fourth straight World Player of the Year award in January, is three goals short of the tally Muller set in 1972 after netting twice in La Liga at the weekend.
"Messi's only thinking about helping the team to win, not about personal records," Barca coach Tito Vilanova told a news conference on Tuesday.
"If he was thinking the other way he would have asked me to play in the Cup."
Holders Barcelona host third-tier Alaves in a last-32 second leg at the Nou Camp on Wednesday when they will defend a 3-0 lead.
Vilanova left out first-team regulars such as Messi, Victor Valdes, Andres Iniesta, Xavi and Gerard Pique when naming a 16-man squad, while calling up a number of Academy players.
"We have given the players who have played the most recently a rest," Vilanova said. "It will be a good game for those just back from injury such as Thiago [Alcantara], Adriano and the players from Barca B."
Spain striker David Villa returned to the side after missing Sunday's trip to Levante with an ankle problem, though he has yet to be given the go-ahead to play by the club's medical services.
"David's fine. We'll see how he is tomorrow but there shouldn't be a problem with him playing," Vilanova added.
The unbeaten La Liga leaders moved 11 points clear of champions Real Madrid at the weekend, after Jose Mourinho's men were surprise 1-0 losers at Real Betis.
Real's third league defeat in 13 games, and the prospect of a city derby against second-placed Atletico Madrid on Saturday, has upped the pressure on Mourinho, but Vilanova side-stepped any comment on their arch-rivals.
"I know you find it hard to understand but my priority is tomorrow's game and later the visit of Athletic Bilbao," Vilanova said. "What happens with other clubs is nothing to do with me."
Get the best features, fun and footballing frolics straight to your inbox every week.
Thank you for signing up to Four Four Two. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.