The World Player of the Year took his Barca tally to 202 goals from 286 appearances in the 4-0 victory away to Viktoria Plzen, putting the holders into the last 16 of the competition with two games to spare.
"Messi will pass Cesar [Rodriguez] to become the top scorer in the history of the club, I consider it a done deal, and I don't rule out that it will happen this year," Barca coach Pep Guardiola told reporters.
"And he's only 24. This says it all."
Spain striker Cesar scored 235 official goals for Barcelona between 1942-55 and his total is within reach during this campaign for the Argentine on current form.
Messi, top scorer in the Champions League over the last three seasons, bagged 53 goals in all competitions last season and this year has already hit 22, including strikes in Barca's Spanish and European Super Cup wins.
So accustomed to seeing him score regularly, when Messi went three games without finding the back of the net last week local media speculated that he was out of form and needed a rest.
His response has been to score consecutive hat-tricks against Real Mallorca in La Liga on Saturday and again in the Czech Republic on Tuesday, when he was also shortlisted as a candidate for World Player of the Year again.
Messi has won the award the last two years.
"There aren't enough adjectives to define him," Barca President Sandro Rosell said. "He's the best in the world. I don't know where his limits are."
