Ref Clos Gomez delayed the start of the match for almost a quarter of an hour, harshly sent off coach Pep Guardiola and striker Zlatan Ibrahimovic and incorrectly awarded a free-kick to Barcelona which led to their first equaliser.
Domingo Cisma had put Almeria ahead after 12 minutes, with the home side's second coming 12 minutes into the second period via a Carles Puyol own-goal.
But Lionel Messi's double gave 10-man Barca a point.
On his dismissal, Guardiola said, "Ask the referee why.
"It was an entertaining game. We created chances, and I should congratulate the team because they never gave up.
"At times when you have ten men, the opponent tries to go for the win. In general, we found it difficult to play against a well organized and motivated team.
"They had chances with Piatti and Crusat.
"I am not unhappy."