A Labour spokesman said the leader’s motion passed by 22 votes to 12 on Tuesday afternoon, meaning it is now down to Mr Corbyn to decide whether to run as an independent candidate.
Mr Corbyn, the veteran left-winger who has represented Islington North since 1983, had criticised the move as “undermining the party’s internal democracy” before its approval.
The motion says he “will not be endorsed by the NEC as a candidate on behalf of the Labour Party at the next general election”.
If Mr Corbyn runs as an independent in the north London constituency where he retains significant support it could cause a distracting challenge for Sir Keir at the next election.
The motion cited the dismal defeat Mr Corbyn led Labour to as leader in the 2019 general election in arguing his candidacy should be blocked.
Labour’s chances of winning the next election and securing a majority in the Commons would be “significantly diminished” if Mr Corbyn was endorsed, it argued.
The move will not be welcomed in all wings of the parliamentary Labour Party, where Mr Corbyn retains the support of those aligned with the Socialist Campaign Group.
MP Nadia Whittome, who has served on Sir Keir’s frontbench, described the motion as “divisive, an attack on party democracy and a distraction”.
Activist Jon Lansman, the co-founder of the Corbyn-backing Momentum pressure group, suggested the Labour leader was acting like an “authoritarian”.
“Keir Starmer unfortunately is behaving as if he was some kind of Putin of the Labour Party. That is not the way we do politics,” he told Times Radio.
However, Mr Lansman said it would be a “big mistake” for Mr Corbyn to run as an independent, saying he wants to see Sir Keir form a Labour government.
Mr Corbyn remains a member of the Labour Party but has lost the whip, meaning he is sitting in the Commons as an independent.
He was suspended over his response to the Equality and Human Rights Commission finding Labour under his leadership was responsible for unlawful acts of harassment and discrimination as he struggled to tackle antisemitism.
The equalities watchdog lifted Labour out of two years of special measures last month, in what Sir Keir called an “important moment in the history of the Labour Party”.
Sir Keir then promptly announced he would bar his predecessor before bringing the formal motion sealing his fate on Tuesday.