Until now, the town hall had been considered the 'most threatened' of the five London town halls on EH's Buildings at Risk register.
The cash will go towards a plan to rescue the 1881 building - built by A&C Harston for a cost of £10,000 - and transform it into a community, local-history and business centre.
The building has been standing empty for some years and has been on EH's register since 2001.
Since 2004 the building - which was the site of one of Clement Attlee's last speeches as prime minister - has been managed by the Limehouse Town Hall Consortium on lease from the London Borough of Tower Hamlets.
The Victorian building is currently used by a number of small arts and creative businesses, but is in a poor condition and suffering from structural problems and damp.
Paddy Pugh, head of advice and grants for the London Region at English Heritage, said: 'There are currently five town halls on the Buildings At Risk Register for London - and Limehouse is in the worst condition of all.
'I am delighted that English Heritage has now been able to help secure the future of this historic landmark of London's East End with a repair grant.
'The imaginative and creative end-uses proposed for the building will put the heart and soul back into Limehouse and enable local people to share in and appreciate its fascinating history.
'This is an exemplary project in a neglected part of London that is now beginning to be transformed by public and private investment. English Heritage is proud to be involved in that process,' he added.