Mr Lapid's comments during a press briefing on Sunday came after more than a week of violence at the site in occupied East Jerusalem, which left more than 200 Palestinians injured by Israeli security forces.
“Muslims pray [there], non-Muslims only visit,” he said. The disputed site is considered the holiest place in Judaism and third-holiest in Islam.
“There is no change, there will be no change — we have no plans to divide the [site] between religions,” Mr Lapid told journalists.
Palestinian Muslims have been angered by an increase in the number of Jewish visits to the compound, where by long-standing convention Jews may visit but are not allowed to pray. Tensions over the visits have been heightened by the overlapping of the Muslim holy month of Ramadan and the week-long Jewish observance of the Passover, which ended on Saturday.
The violence in occupied East Jerusalem raised fears of another Israeli-Palestinian conflict, similar to the 11-day war last year between Israel and the militant group Hamas in the Gaza Strip, caused by similar unrest at Al Aqsa.
Israeli Prime Minister Naftali Bennett spoke with US President Joe Biden and “updated him on the efforts to stop the violence and incitement in Jerusalem”, his office said.
Mr Biden accepted a prior invitation by Mr Bennett to visit Israel and said during the call that he would do so in “the coming months”, it said.
Palestinian officials and militants have repeatedly accused Israel of seeking to divide Al Aqsa into Jewish and Muslim sections or visiting times, as with another sensitive holy site in nearby Hebron.
They have voiced anger at repeated incursions by Israeli security forces into the mosque compound.
But Mr Lapid blamed renewed tensions at the site on “terrorists” trying to incite violence.
“Terrorist organisations have been trying to hijack the Al Aqsa Mosque in order to create an outbreak of violence in Jerusalem and from there a violent conflict across the country,” he said.
He accused Hamas, which rules Gaza, and Islamic Jihad, another militant group in the Palestinian enclave, of sending “extremists” with weapons and explosives to use the Al Aqsa compound “as a base to incite violent riots".
“They have done this to create a provocation, to force the Israeli police to enter the mosque and remove them,” he said.
“The only reason police have entered the mosque in recent weeks is to remove them.”
Israel on Saturday announced an indefinite closure of its only civilian crossing from the Gaza Strip in response to rockets fired from Gaza. The crossing is used by about 12,000 Palestinians in Gaza who have permits to work in Israel.