Gourcuff missed coach Laurent Blanc's final cut along with young defender Mapou Yanga-Mbiwa, who helped Girard lead Montpellier to their first Ligue 1 title last season.
While Girard described his protege's omission as a "semi-surprise" he said he had been caught out by the decision to leave Lyon midfielder Gourcuff behind.
"The team that Laurent has chosen seems to be balanced. That said I was still a little surprised by the exclusion of Gourcuff," he told L'Equipe.
"Since he brought him in to the original 26-man squad I thought he might take him until the end. If he had not been in the 26 then I would not have been as surprised."
The Lyon midfielder's place in France's squad has been up in the air after he endured an injury-interrupted season.
But after forcing his way back in Gourcuff, who played under Blanc for two seasons at Bordeaux, seemingly spurned his chance to impress during the weekend's 3-2 win over Iceland.
The 25-year-old came under fire as Les Bleus came from 2-0 down, after Gourcuff's 75th-minute substitution, to avoid an embarrassing defeat.
"The press were very critical of him and that's unfortunate," Girard said.
"The problems in that game were not solely Yoann but the collective effort of the team. At the same time a lot is expected of him.
"Personally I do not think that game changed anything. The dice was rolled. We must move forward now."
Asked whether Blanc should have included Gourcuff at all, he added: "The media would have questioned Laurent if he did not call him up. It would have been a topic of conversation.
"A decision had to be made. Laurent has selected the players he think can do the job now."
That selection meant the 23-year-old Yanga-Mbiwa also missed out but Girard said he expected the sought-after central defender would bounce back.
"It is a semi-surprise but he is still only young," he said.
"He is on the rise, but he is surely going to be disappointed.
"It's is tough but I do not worry for him. Next year when he is playing Champions League for us, or somewhere else, he will continue to grow. He is a strong beast."
Blanc's decision to overlook Yanga-Mbiwa, who has been linked with moves to Arsenal and Newcastle this summer, means France will take just three recognised central defenders to Poland and Ukraine.
It is a situation Girard admitted was slightly perplexing, with France's full-backs unlikely to provide the cover if needed.
"I don't know why he has taken three central defenders. Maybe Laurent has an ulterior motive," he said.
"When there was (Eric) Abidal it was easier to balance the team.
"I can not see (Patrice) Evra, (Gael) Clichy or (Mathieu) Debauchy coming into to cover in the heart of defence."
France open their Euro 2012 campaign against England in Donetsk on June 11.