Giroud has scored five goals in his past six internationals, but is still seemingly yet to win over the fans.
With his team preparing to host the Euros, Deschamps said the criticism of the 29-year-old was unwarranted.
"You hear what you want. The whistles were unfair tonight, but in Biarritz, he was applauded. People can be conditioned," he told reporters.
"But Olivier scored again. When you say it, you are not helpful. You are free to say what you want but this is not necessarily the truth."
Another player who netted was Dimitri Payet, who curled in a dramatic 90th-minute free-kick to see France to their win.
Deschamps lauded the West Ham star and said the midfielder had developed into a crucial player for his nation.
"It's been three weeks since he played," he said.
"This game was good for him, to get back into the pace. He can do better, but every time he touches the ball, there is something happening. And he has the quality of set-pieces, free-kicks, corners and it is something important.
"He is very important."
France take on Scotland on Saturday before kicking off the Euros against Romania on June 10.