The westbound lanes were closed just after 8 p.m. Friday so crews can work on reconfiguring lanes on the upper deck, as well as pave the roadway and paint stripes for new lanes.
Caltrans says the westbound direction is scheduled to open at 5 a.m. Tuesday, as long as the weather cooperates, with no heavy rainfall.
The National Weather Service says a weather system is approaching the region, but is forecasting only a 20 percent chance of showers on Monday.
While the roadway is closed, BART is running limited all-night service early Saturday, Sunday and Monday mornings, and local ferries will also be adding service.
Heather Ishimaru and the Associated Press contributed to this report.