In an attempted show of strength, the Islamic fundamentalist Hamas and Islamic Jihad groups tried to enforce a two-day strike in Gaza to protest the bloodshed.
But most Palestinian merchants opened their shops after PLO police removed roadblocks of burning tires and boulders set up by militants.
The strike was observed in the West Bank, most of which is still occupied by Israeli soldiers.
Sunday's clashes deeply shook the fledgling trust between Israel and the PLO.
During the four-hour riots, Palestinian police and Israeli troops fired on each other, violating a basic tenet of the peace accord that the two forces must coordinate and cooperate if the self-rule experiment is to work.
But the violence, the worst since the start of self-rule in May, also underscored the resilience of the agreement.
Israelis and Palestinians began talks in Cairo on Monday, as scheduled, on expanding self-rule to the rest of the West Bank.
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