Eight people have died over the last two days
"The Palestinian high court has decided to release two senior members of the PFLP (Popular Front for the Liberation of Palestine), Rabah Muhanna, and Yunis aj-Jaru, immediately," their attorney, Raji al-Surani, was quoted as saying.
Early on Wednesday, Israeli troops continued their staggered withdrawal from autonomous Palestinian towns in the West Bank, pulling out of the commercial and political centre Ramallah after an incursion of almost three weeks.
Incidents of violence continued to erupt elsewhere in the West Bank and Gaza Strip however, claiming the lives of two Palestinians.
Israeli undercover forces fired at three Palestinians in the West Bank town of Yatta, killing a 50-year-old man who was suspected of killing a Jewish settler several years ago, Palestinian officials said.
And a Palestinian was also killed and five were wounded by Israeli fire near the Khan Yunis refugee camp in the Gaza Strip, Palestinian security officials said.
The army said it was returning fire after three mortar shells were shot at the Jewish settlement of Neveh Dekalim.
PFLP release
The Palestinian Authority arrested dozens of PFLP members and outlawed the group's armed wing, which said its men had killed Zeevi, but it rejected Israel's demand to hand the suspects over to the Jewish state.
The BBC's Barbara Plett in Gaza says the two leaders whose release has been ordered are prominent figures in Gaza. Mr Aj-Jaru is a lawyer and Mr Muhanna heads a health agency.
One PFLP member, though pleased by the outcome, said she was not optimistic that it would be any more than a symbolic victory.
Barbara Plett says the decision does put further pressure on Yasser Arafat, with Israel demanding the arrest of Zeevi's assassins and a list of other militants.
So far he has avoided confronting the armed militias by detaining mostly members of their political wings.
This has angered both Palestinians and Israelis - Palestinians because they see these people as intifada activists and community leaders; Israelis because they want him to go after the men with the weapons.
Israel's withdrawal
Israel's withdrawal from Ramallah followed a day of violence elsewhere in the West Bank which left six people dead - five Palestinians and an Israeli soldier.
Israel's defence ministry says it will maintain a security blockade around Ramallah - the seat of Yasser Arafat's Palestinian Authority in the West Bank - after the withdrawal.
Israel has already pulled out of three towns - Bethlehem, Beit Jala and Qalqilya - in the past week, following intense pressure from the US.
It is not yet known when Israel plans to withdraw from Jenin and Tulkarm. All the invasions occurred after Zeevi's assassination in October.
The defence ministry statement said that while withdrawing from central Ramallah the army "reserves the right to act freely and to continue to launch all necessary operations... to foil attacks".