The Spanish champions' failure to get all three points could cost them dearly, as they remain a point behind leaders Real Madrid who still have two games in hand.
Barcelona had been second best for much of the encounter in Andalusia but clicked into gear right after Alex Alegria's opener, throwing themselves forward in search of an equaliser.
They thought they had it when Aleix Vidal's cross was turned in by Jordi Alba despite Aissa Mandi's clearance.
But Hernandez contentiously ruled it out despite the furious protests of Barca's players, and ruled out another effort that Mandi got back to in time again moments later.
Luis Suarez eventually ensured a share of the spoils right at the death but the result left a poor taste in the mouth of Luis Enrique's men, with Neymar mocking the match official on Instagram.
The Brazil star first drew reference to the wrongly disallowed goal, scrawling "HAHAHAHAHAHA" over an image of a replay clearly showing the ball had gone over the line.
He then published another image of a Betis defender wrestling him to the ground in the goalmouth scramble, captioning it: "Had to be a penalty."
The failure to award a legitimate goal could have long-standing implications on the destination of the La Liga title at the end of the season.
Barcelona's Clasico rivals Madrid entertain Real Sociedad later on Sunday having played a round fewer, with their head-to-head record against the Catalans leaning slightly in their favour after last December's 1-1 draw at Camp Nou.