Palestinian officials said the clash involved local residents hurling stones at the Israeli troops in the village of Kafr Malik, just outside of Ramallah.
The Israeli military said the Palestinian man threw a firebomb at the Israeli jeep, causing it to swerve and hit him.
The military said soldiers later tried to provide medical assistance to the man, but the Palestinian had already died from his wounds.
Majid Maadi, the mayor of Kafr Malik, identified the dead Palestinian as Abdallah Ghanayem, 22.