Barca trailed to goals from Kevin Gameiro and Daniel Parejo until Messi intervened, scoring twice to earn the champions a point at Camp Nou.
But despite Messi's 11th goal in his last nine matches in all competitions, Barcelona's run of eight successive La Liga wins came to an end against an excellent Valencia side, who stunned the hosts early on.
Barcelona coach Ernesto Valverde remains hopeful Lionel Messi will be fit to face Real Madrid on Wednesday, despite the striker feeling a "small problem" during Saturday's 2-2 draw with Valencia.
Aside from the quality of the strike, football fans also enjoyed Messi's reaction.
Lionel Messi celebrates a goal for FC Barcelona.
Asked what the problem was, Valverde said: "I don't know, I would like to tell you more but I don't know exactly".
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"We'll wait to see what the doctors say, then evaluate things based on that".
He has now scored in 8 consecutive La Liga matches for the third time. Two minutes into the game they attacked along Barca's left, weakened because Sergi Roberto was playing in place of Jordi Alba.
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.
Valencia were weakened when Gameiro departed injured after 40 minutes.
Although Messi returned to the pitch minutes later, he looked to be in some discomfort, but Valverde is not fearing the worst, suggesting that the player could still be available for Wednesday's crucial first-leg semi-final tie against rivals Los Blancos.
Messi pulled one back before the break and levelled the scoring with a carefully placed shot from outside the box in the second half.
Real Sociedad won the Basque derby 2-1 at home to Athletic Bilbao to move to eighth in the table.