The polls were held on Tuesday.
The opposition, mainly the Samajwadi Party, also won some seats.
Election Commissioner for the polls, P. K. Mohanty, said that the elections were countermanded due to certain complaints at 11 places.
While the BJP leaders claimed that the party's popularity was behind its 'historic win' as opposition candidates dared not to contest, the opposition claimed that the state machinery had hijacked the elections.
The Congress could manage a single victory in Jagdishpur which is part of Amethi, the pocket borough of the Gandhi family, where Rahul Gandhi lost to Smriti Irani in 2019 Lok Sabha elections.
Among other prestigious seats won by opposition parties were in Varanasi, Ballia, Ghazipur and Etawah.
Pragatisheel Samajwadi Party Lohia (PSPL) president Shivpal Yadav, who has been the chairman of the bank for three terms since 2005, said that the BJP government brought about changes in the rules which disqualified him from contesting.
"Contesting for the chairman's post for over two times is now barred. The new rule is designed to keep the opposition at bay and is undemocratic," he said.