The 36-year-old suspect was held on suspicion of a racially motivated assault, and the nun suffered a bruised forehead, police said.
He is due before Jerusalem Magistrate's Court for a detention hearing, as the French Biblical and Archaeological School and Hebrew University condemned the assault.
The incident adds to strains over Christians' treatment in Israel, following Easter access disputes at the Holy Sepulchre and years of harassment in Jerusalem's Old City.
With far-right politicians emboldening extremists, can Israel reverse the growing exodus of its young Christian population?
As attacks on Christians escalate, has the historic agreement protecting Jerusalem's holy sites effectively collapsed?