Frenkie De Jong, Francisco Trincao, Coutinho joined skipper Messi in the Catalans line-up while there was no sight of Luis Suarez.
Barca started guns blazing six minutes from kick-off after a short corner found Coutinho, who rattled the crossbar following a deflected shot.
It was the Catalans who threw the first punch on 21 minutes after Coutinho finished off a flowing passing move involving Antoine Griezmann, Messi and new signing Trincao.
Following a promising spell, Girona were on the back-foot again soon after the half-hour mark as Coutinho's strong attempt from a distance had Girona goalkeeper Juan Carlos pulling off a save.
Messi doubled his side's lead in the final minute to halftime after playing a one-two with Coutinho outside the area before firing in off the far post.
Girona were given a lifeline immediately after halftime following a well-taken finish by Samu Siaz off an equally solid assist by Jairo.
Howevr, the Catalans regained their two goal advantage on 51 minutes when a move down the right picked out Messi whose shot deflected off the defence and into the net.
Wholesale changes from Barca on 60 minutes had Nelson Semedo, Clement Lenglet, Junior Firpo, Riqui Puig, Carles Alena, Ousmane Dembele, Pedri, Konrad de la Fuente and Martin Braithwaite entering.
Konrad opened up the visiting side following the closing phase as a solo run found Pedri in a promising position, but Carlos was on hand to deny the youngster.
Barcelona still pushed for a fourth as full-time loomed, but could not find the desired finishing touch as it finished 3-1 in Catalonia.