Dozens of people, most of them Muslim worshippers, were wounded on Sunday in confrontations between Israeli police and Palestinians in and around the holy site revered by Muslims as al-Haram al-Sharif and by Jews as the Temple Mount.
"Jerusalem belongs to its Arab inhabitants, Muslims and Christians. The future (of the city) will not be settled at the negotiating table but on the ground of confrontation and resistance," Meshaal said.
The Arab peace initiative offers a road map for normalisation of ties between Arabs and Israelis in return for an Israeli pullout from occupied Arab lands.
Saudi Arabia launched the initiative in 2002.
Meshaal has called for rallies to express rage and solidarity with the Palestinians staging a sit-in inside al-Aqsa mosque, and addressed Recep Tayyip Erdogan, the Turkish prime minister, in particular to intervene to protect the mosque.
Regarding political settlement with Israel, Meshaal said that the US, under President Barack Obama, had failed to convince Israel to halt settlement activities for a year.
He said the Obama administration adopted the Israeli demand for Arab countries to recognise Israel as a Jewish state.
Aziz al-Dweik, speaker of the Palestinian Legislative Council, told Al Jazeera that "the occupation is going on with its scheduled plan to demolish the al-Aqsa mosque, God forbid it, and to keep prayers away from it."
Speaking to Al Jazeera from the West Bank city of Hebron, Dweik said that the Palestinian-Israeli negotiations process "gives the occupation a green light to continue messing with our capabilities and sanctities".
"I ask the [Palestinian] negotiator if he has managed, through negotiations, to prevent the aggression against and the desecration of the al-Aqsa mosque," he said.