Araujo steered in a Frenkie de Jong pass across goal in the 92nd minute to end Barcelona’s two-match losing run and spark wild celebrations.
Pedri gave the hosts the lead at the Estadi Olimpic Lluis Companys with a low shot from the edge of the area which clattered in off a post.
But Girona were soon level against the run of play through Axel Witsel’s fantastic overhead kick following a corner.
Barcelona had plenty of chances to regain their lead, mostly through Marcus Rashford, who saw a free-kick hit the bar in the first half.
The Manchester United loanee also had a glorious chance in the second half but could only turn a low cross wide of the target from a few yards out.
Hansi flick will miss Barcelona’s next league match, against Real Madrid in El Clasico on 26 October at 15:15 GMT.
