The Arsenal striker was jeered despite scoring in the 3-2 victory - taking his personal record to five goals in his past six international appearances.
With Karim Benzema not available for Euro 2016 due to an investigation into a sex-tape plot involving Les Bleus team-mate Mathieu Valbuena, Giroud may lead the line for the tournament hosts when they open their campaign against Romania on June 10.
But he faces a battle to win over the fans prior to the Stade de France clash.
He told reporters following the game in Nantes: "Yes, I heard them [the boos].
"I don't know. You know I've had difficult moments that have been difficult to manage in my career, so these don't affect me, but it's a shame.
"Being French, playing for France, if you miss a chance you expect your fans to encourage you. That's what they're there for.
"In any case, I scored a goal with my only shot. So I don't really understand it, but the important thing was that we won, and I've continued my little personal run."
Head coach Didier Deschamps was equally baffled at Giroud's treatment and described the fans' jeers as "unfair".