JERUSALEM — Throngs of Muslims resumed praying at the Aqsa Mosque in Jerusalem on Thursday after Israel, seeking to reduce tensions in an explosive atmosphere, removed the last traces of security structures near the entrances to the holy site before dawn.

The moves came after a two-week standoff and outbursts of deadly violence that had spread to the West Bank, as Palestinians in East Jerusalem boycotted the sacred compound, praying en masse in the streets to protest the installation of metal detectors and other security measures.

Amjad Idris, 21, a municipal worker from East Jerusalem, said that the Palestinians had won.

“All is good,” he said. “What the Israelis put up yesterday has gone today.”

But emotions remained charged, and clashes broke out in and around the holy esplanade. Protesters hurled stones and were dispersed by the riot police. Palestinian medics reported dozens injured by stun grenades, tear gas and rubber bullets.