The Argentine forward netted the only goal as Barca survived a tricky night away to Shakhtar Donetsk, giving his side a 6-1 aggregate victory, and took his tally for the season to 48 goals from 46 games in all competitions so far this season.
Messi set a new club record, passing the 47 scored in 51 games by Brazilian Ronaldo during Barca's 1996/97 campaign under Bobby Robson.
The World Player of the Year is the Champions League's leading marksman so far with nine goals, a title he is on course to claim for a third year in a row, has notched 29 in La Liga, seven in the King's Cup and three in the Spanish Super Cup.
He has the chance to add to his tally as Barca still have 10 matches left to play this season, or 11 if they make it to the Champions League final in London next month.
It is not only the quantity of goals but the importance of his interventions for the squad as a whole that counts.
In a nervous league encounter against lowly Almeria on Saturday he levelled from the penalty spot minutes after the visitors had stunned the Nou Camp with a shock breakaway goal.
He sealed a 3-1 win by forcing an error to score and kill off Almeria's chances of a late equaliser, and on Tuesday helped Barca avoid any slip ups in Ukraine.
"Messi gives us much more than goals," Barca goalkeeper Victor Valdes told reporters.
"He helps the team in defence and in attack. His work is positive for everyone."
Messi's form is a boost to Barca's confidence ahead of their trip to play league title rivals Real Madrid at the Bernabeu on Saturday, and their meeting again in Valencia four days later for the King's Cup final.
They are also set to play Real in the Champions League semis on April 27 and May 3, if Jose Mourinho's side successfully defend their 4-0 quarter-final first leg advantage over Tottenham at White Hart Lane on Wednesday.
Valdes had an inspired game in goal against Shakhtar and keeping a clean sheet was another plus point for Pep Guardiola's team, especially considering their problems in defence.
Argentina midfielder Javier Mascherano was a surprise partner for Gerard Pique at centreback, as Guardiola shuffled his squad in the absence of the injured Carles Puyol and Eric Abidal.
Guardiola's only other options for the run-in are the little-used Gabriel Milito, another midfielder Sergio Busquets or someone from the youth team.
"Mascherano is a quick player and very intelligent," Pique told reporters. "He is capable of adapting to any position."
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