Work on the Zim Piraeus was completed by about 4 a.m. after days of protests and union members refusing to unload the ship because of a heavy police presence, International Longshore and Warehouse Union spokesman Craig Merrilees said.
Protesters against Israeli military action in the Gaza Strip have maintained a constant presence at the port since hundreds marched in on Saturday afternoon.
They drew inspiration from a 1984 action when ILWU members refused to unload ships moored in San Francisco carrying South African cargo, comparing the relationship of Israel to Palestinians in the Gaza strip to the apartheid regime in South Africa.
The ship, which is owned by the Israeli shipping company Zim Integrated Shipping Services, docked at the port on Sunday evening but dockworkers would not cross picket lines outside of the gates for safety reasons.
Merrilees said that dockworkers did not want to work with a heavy police presence, citing previous problems between police and the union such as a 2003 incident when Oakland police fired rubber bullets at war protesters at the port and wounded workers there.
On Tuesday night, the protesters briefly declared victory as the ship left Oakland and marine tracking services showed it leaving the Bay Area en route to Los Angeles. But a few hours later it returned and moored at a different terminal.
Longshore workers reported there and found the number of protesters and police had dwindled enough that they could safely unload the ship. They got started at about 10 p.m. and finished up at about 4 a.m.
While the ship was eventually unloaded, protesters are calling the days of delay a victory for their cause.
"Zim has undoubtedly suffered significant economic losses, and we have set a powerful precedent for what international solidarity with Palestine, through boycott, divestment, and sanctions, can look like," protester Reem Assil said in a statement today.
The Jewish Community Relations Council issued a statement earlier this week calling the protest "an overt expression of extremism, extremism that is alienating to the vast majority of Bay Area citizens including our community and has no place on our coast or anywhere else."
"Sadly, this is one of many instances in which Israel has been unjustly singled out. As millions face discrimination, torture and death at the hands of ISIS, Syrian militia and other ruthless leaders and oppressors both in the Middle East and elsewhere, Israel continues to be placed under a microscope despite the egregious human rights violations taking place in countless other countries," the statement said.
According to Oakland police spokeswoman Officer Johnna Watson, there were no arrests during the demonstrations but police issued two citations Monday morning for blocking the street.
Protesters in Long Beach and Seattle have planned similar actions targeting other Zim-owned ships later this week.