The Argentina global scored twice, once from the penalty spot, as the hosts came from 2-0 down to earn a point and extend their lead at the top of La Liga to six points.Kevin Gameiro put Valencia ahead and Dani Parejo added a second goal by converting a penalty.
Valencia had two golden chances to make the breakthrough in the first three minutes, but Parejo saw his close-range effort saved by Barcelona goalkeeper Marc-Andre ter Stegen, before Denis Cheryshev smashed the rebound off the post.
Lionel Messi celebrates a goal for FC Barcelona.
Kevin Gameiro and Dani Parejo scored in the 24th and 32nd minute respectively to stun the Blaugrana.
The coach also played Sergi Roberto at left-back instead of Jordi Alba, who is having a sublime season, and Thomas Vermaelen next to Gerard Pique, resting Clement Lenglet.
Valencia were weakened when Gameiro departed injured after 40 minutes.
They doubled their lead eight minutes later after a push from Roberto saw a penalty awarded. But their advantage was short lived after Lionel Messi converted a first-half penalty.
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He has now scored in 8 consecutive La Liga matches for the third time.
Little did it matter that the team's all-time leading scorer had just struck two goals to lead Barcelona back from a two-goal deficit to secure a 2-2 draw.
Earlier, TUKO.co.kereported that Philippe Coutinho has applauded Lionel Messifor handing him the responsibility to take the morale-boosting spot-kick that helped Barcelona thrash Sevilla to claim a semi-final spot in the Copa del Rey.
The result sees Barcelona move six points clear of second-placed Atletico Madrid at the top of the La Liga with Valencia toppling Real Sociedad in the seventh spot.
There was some concern over Messi five minutes later when the Argentine appeared to suffer a blow to his thigh, which required some treatment on the touchline, but he did eventually return to the field.
Barca's insatiable captain equalised in the 64th with an unstoppable curling strike from outside the area, averting a first league loss for the league leaders since November and taking them on to 50 points from 22 games.