The soldiers "responded with defensive fire" against the assailant, France's Interior and Defence minister said in a statement, shortly after the attack.
On Friday, a driver deliberately rammed his car at four troops guarding a mosque in the southeastern city of Valence.
One of the soldiers fired back, wounding the attacker in the leg and arm.
The impact of the car also left the soldier with injuries to his knee and shin.
For the time being, investigators are still trying to determine what the driver's motives were; whether he acted out of personal reasons or if he had a political agenda.
"At first sight, what we can say is that the attacker deliberately wanted to harm the soldiers, absolutely not the Muslim community", Frédéric Loiseau, secretary general of the region's police force, told reporters.
France is on high alert after the November 13 Paris attacks that killed 130 people.
In the aftermath, the country has witnessed a spike in anti-Muslim incidents, with mosques being vandalized notably in Corsica. There, a solidarity rally for security forces who had been targeted in an ambush over Christmas, ended with protesters shouting slogans like "Muslims out"!
In Valence, local officials have ruled out any inkling of islamophobia, proclaiming the region to be peaceful. The area where the mosque is located is "calm", Mayor Nicolas Daragon told French radio France Info.
"We're really looking at an isolated incident, there was no tension in particular prior to this", Daragon said.
The soldiers who were standing guard, are part of the reinforced security guarding places of worship and other sensitive sites.
Operation Sentinelle, as it's known, came into force after the January Charlie Hebdo attacks, which saw some 7,000 soldiers descend on the capital and throughout France.
That number has gone up to 10,000, as the country tries to adjust to the heightened terror threat at home.
Yet incidents like what happened in Valence have underscored the dangerous nature of the military's new role. A view acknowledged by France's Defence minister Jean Yves Le Drian.
"Yes they [soldiers] are exposed," Le Drian said on French TV channel BFM-TV.
"This attack shows that Operation Sentinelle is risky. But the courage and composure shown by the four soldiers also indicates why their participation is necessary," he said.