The two Palestinians were hit by rubber bullets and evacuated on stretchers with bloodied legs, an AFP journalist reported.
Youths wearing hoods or masks threw stones at Israeli soldiers, who responded with rubber bullets and water canon containing foul-smelling liquid.
The clashes broke out at a checkpoint at the entrance to Ramallah and near the Israeli settlement of Beit El, the site of regular demonstrations against the occupation.
The protest was called in support of hundreds of Palestinian prisoners on hunger strike in Israeli jails since April 17.
Israel says 300 Palestinian inmates end hunger strike
"We are entering an extremely critical period" for the hunger strikers, Qadura Fares, head of the Palestinian Prisoners Club, said earlier at a rally in Ramallah.
"A large number of prisoners can no longer move from their bed or take care of their basic needs."
The Red Cross visited the leader of the hunger strike, Marwan Barghouti, on Thursday for the first time since it began.
An ICRC spokesman was unable to provide an update on his health "in accordance with the principles of medical confidentiality".
The ICRC had been allowed access to other prisoners on hunger strike, but Israel had been restricting access to Barghouti.
Hunger strikers have issued a list of demands including better medical services, family visits and more dignified detention conditions.
Israel policeman fired for beating Palestinian driver
Israel says conditions meet all international standards.
Barghouti, a senior member of Palestinian president Mahmud Abbas's Fatah party and a highly popular figure among Palestinians, is serving five life sentences over his role in the second Palestinian intifada, or uprising.
Earlier this week, Israel produced footage they said showed him secretly breaking his fast in his cell.
His wife Fadwa rejected the footage as fake, saying it was "intended to break the morale of prisoners".Ramallah
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