Ten members of the Supreme Election Board (YSK) decided against annulling the vote, while only one voted in favour, the state-run Anadolu news agency reported.
The main opposition Republican People's Party (CHP) and the pro-Kurdish Peoples' Democratic Party (HDP) had Tuesday requested the poll be scrapped due to alleged violations.
The 'Yes' camp won 51.41 per cent in Sunday's referendum in a narrower-than-expected victory but the opposition claimed the outcome would have been reversed in a fair poll.
That also sparked protests from individuals who opposed constitutional changes granting Erdogan strengthened executive powers and who formed long queues to submit their petitions.
Bulent Tezcan, CHP deputy leader, said the YSK decision sparked a "serious legitimacy crisis," in an interview with CNN-Turk television.
"We will activate all legal channels," he said, adding that the party would map out its policy after meeting legal experts tomorrow.