Barca's first two goals came from own goals by the hosts, who are in their first La Liga season.
Luis Suarez smashed home the third after latching on to a Sergi Roberto long ball, BBC reports.
Girona, who are co-owned by Manchester City, played five City loanees in the game, with Brazilian midfielder Douglas Luiz impressive in attacking positions.
Pablo Maffeo, in his third season on loan, successfully man-marked Barca's Lionel Messi, who had scored 11 goals in his previous five games, including four against Eibar on Tuesday.