Joan Ostojic's daughters Katherine, 21, and Alice, 19, were on a boat carrying 25 people that went down between Lombok and the Komodo Islands on Saturday.
They sat on the semi-submerged vessel's roof for 10 hours before embarking on their swim, their mother said.
Mrs Ostojic, from Stevenage, said: "It's a relief that they are safe."
She added: "They are fine, carrying on with their travels, and will be home shortly."
Travellers from New Zealand, Spain, France, Switzerland and the Netherlands were among those rescued after the boat hit a reef near Sangeang Api, a volcanic island off Sumbawa, in bad weather during the three-day journey.
Mrs Ostojic said the girls sent an email to her and her husband Peter saying they had heard everyone had been found.
They also revealed that after the boat sank in the middle of the night, they swam for eight hours to the shore before seeing the lights of some fishermen and being rescued, their mother said.
The Foreign Office said Alice Ostojic had been been travelling through Australia and south-east Asia as part of her gap year.
Katherine, who is at Bristol University studying aerospace engineering, had joined her for a month in Indonesia.
After being rescued, the girls spent the night on the nearby uninhabited volcanic island, where they were given food and water by fishermen, before they were taken to Bima in Sumbawa.
The girls lost everything in the accident apart from their passports, debit cards and cash.

Welsh Secretary Stephen Crabb was speaking after Friday's final televised debate before the election.
"There's only one party that's in a position to secure an overall majority and that's the Welsh Conservatives," he told the Sunday Politics Wales show.
During the debate, Labour's Owen Smith clashed with Plaid's Leanne Wood.
Mr Smith challenged Plaid's Leanne Wood about whether she would vote down an Ed Miliband minority government. The Plaid leader responded by accusing Labour of taking Wales for granted over many decades.
Also speaking to Sunday's BBC Wales programme, Mr Smith repeated his call to Ms Wood.
"Hell will freeze over before I vote with the Tories. Leanne Wood hasn't confirmed that she wouldn't vote with the Tories," he stated.
"She's the one that's got a question to answer about that not Labour."
On behalf of Plaid Cymru, Dr Dafydd Trystan said his party's view was absolutely clear: "We will not vote for a Tory prime minister neither will we vote for Tory policies imposed by a Labour Party."
Welsh Liberal Democrat leader Kirsty Williams told Sunday Politics Wales: "The choices are either having a government that is dragged off by nationalists who will threaten jobs and threaten the stability of the union, or dragged off to the right by UKIP that would cut public expenditure or they could choose to vote for the Liberal Democrats who would anchor the government in the centre ground."
UKIP's Nathan Gill told the programme: "We really do believe that the people who make our laws are the people that are in Westminster or the Welsh Assembly, not in Brussels.
"We believe that the money that we spend needs to be spent here in Wales or Britain on us."
Wales Green party leader Pippa Bartolotti said, "We have a very real and immediate problem with the state of gender pay. I want to help women out of this terrible rut that government after government has kicked them into."
Sunday Politics Wales is on BBC One Wales on Sunday 3 May at 11:00 BST - or on the BBC iPlayer.
A mother whose two daughters swam for eight hours to safety when their boat sank in rough seas in Indonesia has spoken of their ordeal.
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The Conservatives have accused Labour and Plaid Cymru of being involved in an "unedifying squabble" over who to support if there is a hung parliament.