A BA franchise airline flight bound for Casablanca in Morocco left Heathrow shortly before 7pm (1800 GMT) on Friday ahead of 30 other international and short-haul evening flights, a BA spokeswoman said.
Mike Street, the airline's director of customer services and operations, said BA faced a complex logistical challenge, with at least 100 aircraft and 1000 flying crew in the wrong place.
"As a result it will take some time to return to a normal flying programme. We recognise how frustrating this must be, but we are working as hard as we can to get customers away on their holidays," he said.
The resumption of flights at Heathrow came shortly after around 1000 BA staff, who walked out on Thursday in support of workers sacked at a catering supplier, returned to work.
Arbitrator ACAS began talks during the afternoon with the union and the catering supplier, Gate Gourmet.
"This is not our dispute. Our customers come first, and everyone involved in creating this unofficial situation must come to their senses," BA Chief Executive Rod Eddington said.
About 620 flights had been
cancelled since Thursday
Around 100,000 passengers fly daily with BA during August, and about two-thirds of its flights, excluding franchises, use Heathrow, the world's busiest international hub.
A BA spokeswoman said 73,000 passengers were grounded on Friday after 40,000 passengers could not fly on Thursday.
Other airlines faced knock-on disruption. Australia's Qantas Airways Ltd said it had cancelled flights, while Finnish national carrier Finnair and Sri Lankan Airlines were also affected.
BA said about 620 flights had been cancelled since Thursday.
BA's relations with staff have been strained since the airline axed thousands of jobs in an industry downturn that followed the September 2001 attacks on the United States.
The latest dispute was triggered by a long-running spat between the TGWU and loss-making Gate Gourmet, which is owned by US private equity fund Texas Pacific.
Unions said Gate Gourmet staff were sacked after they walked out in protest at planned changes to pay and conditions. The company said its reforms were needed to safeguard its future.