The injured soldier was brought to Beilinson Hospital in Petah Tikva for treatment and is now in stable condition, an army spokesperson said.
Masked Palestinian youth burn tires and throw stones in Joseph's Tomb during clashes with Israeli troops nearby, in the West Bank city of Nablus in April 2011.
Sixteen buses carrying Jewish worshipers were accompanied by IDF soldiers, who secured their approved visit to the flashpoint site.
The prayer went on as planned, however several instances disturbed the event, including stone throwers and Molotov cocktails.
The sources said the soldier suffered a moderate injury, and received the needed treatment before he was moved to an Israeli hospital.
Palestinians threw rocks at the buses and the soldiers to protest the arrival of the settlers in Nablus.
The troop was shot near the entrance of the Balata refugee camp, located a few blocks from the tomb on the outskirts of the Palestinian-controlled city.
The tomb, identified as the resting place of the Biblical Joseph, sits on the slope of Mount Gerizim in Nablus, not far from the Balata refugee camp.
Under the 1993 Oslo Accords, Joseph's tomb was to remain under Israeli control.
Two of the Israelis were lightly injured as a result of the rock-throwing and were treated at the scene.
Last week, dozens of members of the Bratslav Hasidic sect were detained by police after they visited the holy site without army escort.
I was a victim of parliamentary boycott, President Rousseff says
Jameson sales continue to grow globally
S.Africa's ruling party says has confidence in finmin Gordhan
ManCity striker Sergio Aguero charged by the FA & Could miss Manchester Derby
Real Money Casino Apps becoming more and more popular
Scuba diver dies after getting into difficulty off Cornish coast
Movies with heroes who play roulette
Senior ISIL Leader, Spokesman Adnani Reportedly Killed in Syria
Queen Beyoncé rules MTV, bags 8 VMA trophies
Mobile gambling market set to be worth 100 Billion by 2017
Bridgewater suffers injury in practice
Aguero charged over Reid elbow
The main reasons why your bet can loose
Microgaming Expanding it's games onto smartwatches
Wayne retained as England skipper
Italy rescues 3000 migrants as arrivals surge
Brazil Senate removes Rousseff from office