The protests started as Muslim men under 50 were prevented from entering the city for Friday prayers.
On the ground, reports posted on Twitter showed the crowds gathering, forming their own prayers, and protesting peacefully.
The Israeli forces released tear gas to disperse the crowd; other reports claim they fired stun grenades. Three Palestinians were reportedly killed in three different areas of East Jerusalem and the West Bank. Up to 400 others were also injured, according to the Palestinian Red Crescent.