The draw confirms Barcelona's lead at the top of LaLiga.
The visitors flew out of the blocks, with Kevin Gameiro handing them the lead on 24 minutes.
Valencia were in dreamland six minutes later as Dani Parejo hammered home a penalty after Sergi Roberto fouled Daniel Wass.
Messi pulled Barcelona back into the tie on 39 minutes, scoring his 20th LaLiga goal of the season, from the penalty spot.
Barcelona took the game to their visitors after the break, and Messi netted an equaliser on 64 minutes, then he injured but there should be no problem as for a short recovery for him.
Both sides had chances to win it in the closing 20 minutes, with Philippe Coutinho curling a free kick just wide, and Rodrigo and substitute Santi Mina forcing saves from Marc Ter Stegen.