About 440 of Muni's roughly 600-vehicle fleet are in operation today and all buses and trains are returning to regular routes, Muni spokesman Paul Rose said.
Cable car service remains out this morning, but might resume in the afternoon, Rose said.
Service has been affected since a large number of Muni workers called in sick Monday and again on Tuesday. Only about a third of Muni's fleet was in service on Monday and about half on Tuesday, Rose said.
The employee union, Transport Workers Union Local 250-A, is in the middle of contentious contract negotiations with the San Francisco Municipal Transportation Agency, although TWU Local 250-A president Eric Williams denied Tuesday that the sickout was organized by the union.
Muni worker strikes were banned by San Francisco voters in a 2010 ballot measure.
Williams said the most recent proposal from the SFMTA includes a pay hike but would require them to contribute to their pensions and would result in a net loss for Muni workers in a city where costs of living are rising.
Members of TWU Local 250-A, which represents about 2,200 Muni workers and other city employees, overwhelmingly rejected the proposal in a vote on Friday.
Rose said under the terms of the city charter, the two sides will now go into arbitration, with the next meeting set for Saturday.
Several city officials, including Mayor Ed Lee, have called for an end to the sickout. SFMTA officials also issued a memo to workers notifying them that they will need to provide a doctor's note to receive sick paid leave or they could face discipline.