The far-right minister had forced his way into the flashpoint site early Sunday under Israeli police protection.
"Any harm to Al-Aqsa Mosque is playing with fire and will drag the region into a religious war with undesirable consequences that will affect everyone," PA spokesman Nabil Abu Rudeineh said in a statement.
He stressed that such acts "will not impose Israeli sovereignty over the site."
The Palestinian spokesman appealed for immediate action from the US and the international community to maintain the status quo at the Al-Aqsa complex.
The status quo allows Muslims to worship at the Al-Aqsa compound and followers of other religions to visit the site.
Since 2003, Israel has allowed settlers into the compound almost on a daily basis with the exception of Fridays and Saturdays.
For Muslims, Al-Aqsa represents Islam’s third-holiest site. Jews call the area the Temple Mount, saying it was the site of two Jewish temples in ancient times.
Israel occupied East Jerusalem, where Al-Aqsa is located, during the 1967 Arab-Israeli War.
It annexed the entire city in 1980 in a move never recognized by the international community.