Hundreds of revellers were evacuated from Mangle E8 in Sidworth Street, Dalston, after police were called at about 01:10 BST.
Officers believe a man threw acid at two men after a dispute between two groups inside the venue.
Two men in their 20s remain in a serious but stable condition in hospital.
Ten other people were were treated for minor injuries, the Metropolitan Police said.
A London Fire Brigade spokesperson said: "The only information that we have is that it was an unknown corrosive substance thrown within the nightclub.
"It was identified by a pH paper test as a strong acidic substance."
It is understood about 600 people were at an event in the club.
Officers said 10 people were taken to hospital by ambulance, while a further two sought treatment at A&E. No arrest has been made yet.