PC Andrew Birks was working at a police station in London when 40-year-old Sean Rigg died in 2008.
He was suspended while the Metropolitan Police carried out an investigation.
Senior officers refused to let him resign until the enquiry was over.
Birks, 39, took his case to the High Court, claiming that the decision was unfair. The Met said if it had let him resign he would have avoided any potential disciplinary proceedings.
A judge dismissed the action brought by the PC and agreed with the police.
He was due to be ordained on 28th September after studying for several years.
Mrs Justice Lang said: "If he is not ordained on that date he will not be able to take up the office of curate in the parish of Portslade, Sussex, and will have to vacate the Church accommodation which he and his partner are already occupying."
In a statement, the Metropolitan Police said: "Our decision to suspend PC Birks, and rescind his resignation, was taken after careful consideration and was based on a unique set of circumstances."
"These included ongoing public interest in the case, the need to maintain public confidence in the accountability of police officers and to allow the IPCC to complete their current investigation.
"We also recognise the personal impact that this decision has had on PC Birks. We respect the decision of the judge today, who has considered all the evidence.
"Six years after Mr Rigg's death, his family and our officers are still waiting for a conclusive outcome.
"There has been much speculation about what took place on the night that Mr Rigg died, but what is important now is that there is a full and thorough investigation based on evidence to finally establish the facts."
The court heard PC Birks wanted to join the priesthood in 2001 but was told to get some experience first so he decided to join the police.
The judge, Mrs Justice Lang, accepted that the case was unusual and said Birk was: "required, against his wishes, to remain a serving police officer for an indeterminate period of time – which I accept could be as long as two to three years if the IPCC finds there is a case to answer – during which time he will not be able to work, either as a police officer or in any other capacity".
She added: "He is being prevented from pursuing his religious vocation to be a minister, for which he has trained for many years."