The two, including a 16-year-old, were detained overnight Thursday-Friday, hours after the incident at Azzoun village in the north of the occupied territory, a Shin Bet statement said.
It said the two Palestinians hid in ambush above the road separating the Maale Shomron settlement from Azzoun before throwing the petrol bomb at a car carrying the Israelis.
The vehicle caught fire and the girl was gravely injured. She was still being treated in hospital late on Saturday, Israeli media reported.
Firebomb attacks by Palestinians in the West Bank against Israeli civilians and military targets are not rare.
According to the military, in the first nine days of December Palestinians carried out 24 Molotov cocktail attacks, five of them targeting civilian Israeli cars.