The minnows hit the woodwork twice before Alex Alegria struck, but Luis Enrique's men saw Jordi Alba's goal moments later wrongly disallowed.
Barcelona missed the chance to temporarily overtake Real Madrid in the La Liga table, slumping to a 1-1 draw at Real Betis on Sunday
The champions pulled within a point of their arch-rivals and the league leaders, who host Real Sociedad later in the day and still have a game in hand to extend their lead.
Betis took charge of the clash early at Estadio Benito Villamarin and hit the woodwork twice through Dani Ceballos and then Ruben Castro.
Alex Alegria struck 15 minutes from time to give the hosts a deserved advantage but Luis Suarez salvaged a draw in the closing stages, after the champions had seen a clear goal not given earlier on.
Complaints from Camp Nou figures over officiating have dominated headlines in recent weeks and the acrimony is likely to continue after the officials failed to spot that Jordi Alba had turned the ball over the line just moments after Betis' opener.
The incident compounded Barca's fortunes, though, with Luis Enrique's side short on ideas and second-best for long spells of the match, in which Betis twice hit the woodwork before eventually finding the net.
That was until the 90th minute, however, when Suarez raced onto Lionel Messi's pass and slotted home to snatch a point.
The visitors will certainly feel justice was done, despite their largely lacklustre display, but leaders Real Madrid could be four points clear with a game in hand if they beat Real Sociedad at the Santiago Bernabeu later on Sunday.
Barca wasted little time in taking the game to their hosts, Suarez seeing a half-volley deflect narrowly wide following Aleix Vidal's deep cross.
Ruben Castro saw a chance go begging when he scuffed the ball straight at the restored Marc-Andre ter Stegen after Lucas Digne had been pressured into conceding possession, but the Germany goalkeeper had to be a little more acrobatic to claw Dani Ceballos' shot away from the top corner.
Barca's play was becoming increasingly disjointed and it was Betis that continued to look the more likely to break the deadlock, but Antonio Adan produced a fine one-handed save to deny Neymar following Lionel Messi's superb throughball shortly before half-time.
The visitors looked a little sharper after the restart, Vidal volleying just past the left-hand post after meeting Messi's cross from the left unmarked.
Betis recovered and continued to frustrate Barca in their approach play, with MSN kept firmly on the fringes of play, and Ceballos was inches from giving them the advantage on the scoreboard with a dipping drive that cannoned off the top of the crossbar.
Luis Enrique introduced Jordi Alba, Sergi Roberto and Gomes from the bench in a bid to inject some intensity into the champions' play but they were again saved by the woodwork when Castro cut in from the left and saw a shot deflect off Gerard Pique and onto the post.
But Betis were not to be denied from the resulting corner. Ter Stegen failed to reach the in-swinging delivery and Alegria turned the ball over the line from Ryan Donk's knockdown despite Pique's best efforts.
Barca were then denied an equaliser by a dreadful decision from the officials. Alba met Vidal's low cross at the far post and steered the ball clearly over the line before Aissa Mandi hooked it away, but referee Jose Hernandez Hernandez failed to award the goal.
Another Vidal centre from the right deflected towards the near post but was just cleared in time by Mandi again, but Castro shot straight at Ter Stegen when he should have made the points safe after being sent through one-on-one.
That missed ultimately proved costly as, in the 90th minute, Messi picked up a loose ball 20 yards out and slid it through to Suarez , who fired low past Adan first time to rescue a point.
