The workers dropped picket lines after arbitrators twice ruled the strike as "not bona fide" because the union was negotiating in bad faith, said ILWU spokesman Craig Merrilees.
That made it impossible for the more than 10,000 longshoremen at the ports to respect the picket lines, said Merrilees.
The ILWU and shipping companies are negotiating to settle a dispute over job security, said Stephen Berry, a representative for 14 shipping companies.
Berry said he was wary about allowing the clerks to return to work without a settlement.
Although the strike came to an end, the two sides are still far apart in their negotiations on a contract to replace the one that expired June 30.
Under the expired contract, the clerical workers had an average salary of 96,000 U.S. dollars, full medical coverage, at least 21 paid holidays, 13 sick days, and four weeks of vacation per year, according to Berry.