The walk-out that started on Monday evening is the second two-day strike this year and the Rail, Maritime and Transport (RMT) union is threatening a further three-day walk-out next week over plans to cut 250 ticket offices and 950 jobs.
Transport for London (TfL), which runs the city's transport network, says the restructuring could save 50 million pounds ($84 million) a year with most passengers now using electronic ticket cards but the union argues that safety and the quality of service will suffer.
The strike, however, failed to stop many of the 3 million commuters using the Tube daily from getting to work, with TfL saying limited services were running on nearly all 11 lines and extra buses were on duty.
But as commuters posted photos of crowded stations, RMT bosses accused TfL of misleading the public over the level of services available and endangering the public with overcrowding trains and platforms.
"It helps no one ... to deliberately mislead the public as to what services are available as it simply piles dangerous levels of pressure onto the ghost trains and skeleton operations, leaving passengers and staff at risk," said RMT acting general secretary Mick Cash.
London Underground's managing director Mike Brown said the level of services was at about 50 percent capacity compared to 40 percent during the last strike in February.
He said 90 percent of the electronic Oyster travel cards that would normally be used on the network were used on Tuesday and two thirds of the city's 274 stations were open.
The walk-out this week only involves the RMT union with three other unions representing rail workers not involved, having accepted a promise of no forced redundancies and that no supervisors would have to reapply for their own job.
Brown urged the RMT to call off further action, saying TfL had already agreed there would be no compulsory redundancies and that safety would not suffer when ticket offices closed, with staff remaining on duty in stations and in control rooms.
No formal talks have been scheduled ahead of next week's action but commuters were hopeful that it may yet be averted.
The Federation of Small Businesses estimated that February's two-day strike cost small businesses, which make up about 99 percent of London companies, about 600 million pounds in lost working hours, business and productivity.
Further action planned for February was averted as the two sides headed back into talks but those negotiations broke down earlier this month, triggering this week's walk-out.
But some politicians and trade union experts said the RMT action was as much political as anything as union leaders compete to establish their militant credentials in the race to succeed former RMT leader Bob Crow, who died suddenly in March.