Valencia, who hit the woodwork in the second minute, went ahead in the 24th with a well-taken finish from French forward Kevin Gameiro and doubled their lead with a powerful penalty from Dani Parejo in the 32nd.
Lionel Messi duly slotted away the spot-kick for his 20th league goal of the season.
However, it was not without cost as he needed treatment for what appeared to be a dead leg shortly after equalising.
Luckily for Barcelona, the 2-2 draw and two points dropped was not punished as Atletico Madrid lost 1-0 at Real Betis on Sunday.
Any hint of Messi being sidelined with the season entering its critical phase with titles on the line immediately overshadowed yet another outstanding performance by the Argentine.
Barca beat Madrid 5-1 in the league earlier this season with Messi missing through injury, but he once again demonstrated his importance against Valencia.
"He is bothered by something but we will have to wait to see what the doctors say", Valverde said.
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Ernesto Valverde rested midfield passing machine Arthur, opting for Arturo Vidal, even though Sergio Busquets was suspended too.
Ter Stegen of Barcelona celebrates after the first goal of his team scored by Nelson Semedo (not in frame) during the La Liga match between Girona FC and FC Barcelona at Montilivi Stadium on January 27, 2019 in Girona, Spain.
With centre-back Gerard Pique off the pitch having a head injury treated, Sergi Roberto sent Daniel Wass tumbling as they challenged for Cheryshev's cross and Parejo converted from the spot.
Valencia were weakened when Gameiro departed injured after 40 minutes.
Messi goal vs Valencia: Lionel Messi pulled things at level on the 64th minute with a brilliant strike. "If he's in good shape, he'll play on Wednesday [against Madrid]". Fourth-place Sevilla has won only one of its last six league games.
MESSI added a second one in the second half, a goal which only he can make look easy.
Fifth-placed Getafe were held to a goalless draw at mid-tabled Levante.