A 25-person rescue team, including members of the police and fire department, searched for the climbers but were hampered by bad winter weather.
At 10.40pm the pair were found near the Hoei crater on the southeastern flank of the mountain. They were then airlifted to hospital via helicopter.
The fire department believed the hikers fell 400m, Asahi reported.
The climate in winter is extremely cold on the 3776m mountain but varies widely depending on elevation.
Temperatures near the summit are -18C, according to Snow Forecast.
March weather is known as a dangerous time to hike. Mountain huts are shut and the season has “strong winds and snowy, icy conditions”, Asahi reported.
Fujisan Climb’s website said off-season temperatures are generally below freezing, making conditions very dangerous.
“From October to around mid-June, climbing to the summit is highly perilous due to extreme wind and weather conditions, snow, ice and a risk of avalanches,” the site said.
Local government guidelines call for prohibiting climbers who are not fully prepared for the climb although many still attempt the climb. Asahi reported there had already been one death on the mountain this winter.
The Ministry of Foreign Affairs and Trade said it is aware of the incident.