"Jordan condemns in the severest of terms the storming of the Aqsa mosque and violating its sanctity," said a statement by the foreign ministry.
Ben-Gvir briefly toured the site under heavy security.
The compound is Islam's third holiest site after Mecca and Medina.
The Hamas resistance movement had earlier warned Ben-Gvir of any wrong action at the mosque as a “red line”.
Lying within Israeli-annexed east Jerusalem al-Quds, the compound is administered by the Waqf Islamic affairs council, with Israeli forces operating there and controlling access.
Waqf guards told AFP that Ben-Gvir was accompanied by units of the Israeli security forces, while a drone hovered above the holy site.
While Ben-Gvir has visited the compound numerous times since entering parliament in April 2021, his presence as a top minister carries far greater weight.
A controversial visit in 2000 by then opposition leader Ariel Sharon was one of the main triggers for the second Palestinian intifada, or uprising, which lasted until 2005.
Source: tbsnews.net