Dutch candidate Boris van der Vorst's hopes of challenging Kremlev for the presidency ended after 106 delegates voted against holding a new election, with 36 voting in favour and four abstaining.
Kremlev was elected unopposed in May after Van der Vorst was declared ineligible. The Court of Arbitration for Sport (CAS) ruled in June that Van der Vorst was wrongly prevented from standing.
IBA, amateur boxing's world governing body, suspended the Ukrainian federation on Friday, leaving it unable to cast a vote. The federation had written to IBA members on Thursday calling for Kremlev to resign or be voted out of office.
The extraordinary congress was delayed for an hour due to a power failure.
Sunday's decision cast new doubt over the sport's efforts to preserve its Olympic spot beyond 2024.
IBA, formerly known as AIBA, was stripped of involvement in last year's Tokyo Olympics due to governance, finance, refereeing and ethical issues.
Boxing is not on the initial programme for the Los Angeles Games in 2028. The IOC is managing the Paris 2024 competition.
