Officials had pushed the reopening to 5 a.m. Wednesday after crews discovered a crack Saturday while conducting seismic upgrades on the 73-year-old bridge.
The bridge, which carries about 260,000 vehicles a day between San Francisco and heavily populated cities to its east, was closed over the Labor Day weekend so a football-field-sized, 3,300-ton section of the eastern span could be cut out and replaced with a new double-deck section.
The new section connects the bridge with a short detour that will be used until a new east span is completed by 2013.
Crews used the opportunity to inspect the bridge and found a 2-inch-thick steel link cracked halfway through.
Ney said a contractor worked throughout Monday night to make a replacement part and complete the work. An inspection following the repair "went without a hitch," he said.
"With those two things we were able to cut back time significantly," he said.
The bridge shut down Thursday night, and other bridges and public transportation systems were able to accommodate extra riders Friday, the first time that the bridge was closed on a working day since a major earthquake in 1989.
But since that was the beginning of a long holiday weekend, Tuesday's morning rush hour could prove more difficult.
Public transit agencies said they plan to increase capacity to handle the expected increase in riders because of the bridge's closure.
Bay Area Rapid Transit spokesman Jim Allison said the commuter rail line will run longer trains, but warned that finding parking at stations may be difficult.
The transit line, which typically carries about 340,000 commuters a day, could see a record day.
"Most people travel to work between 8 and 9 o'clock. If you can avoid that hour, that's a good idea," Allison said.
The Golden Gate Transportation District said the Golden Gate Ferry will add one morning vessel with a capacity of 715 passengers, to leave Larkspur for San Francisco.
