The 66-year-old - dubbed the Crystal Methodist - admitted a charge of "seriously impairing the mission, witness or integrity of the Church" during a disciplinary hearing last month, the church said.
Flowers was suspended by the church in 2013 following allegations that he bought and used illegal drugs.
He now been removed from the roll of ministers following an appeals period - meaning he can no longer use the title reverend or lead services.
Flowers stepped down as chairman of the Co-operative Bank amid the claims of illegal drug use and inappropriate expenses payments four years ago.
He was secretly filmed handing over £300 in cash for drugs in 2013 and admitted being in possession of cocaine, crystal meth and ketamine at Leeds Magistrates' Court in May 2014.
The court heard that he had been a "cocaine user for the past 18 months" and "cited stress and the care of his terminally ill mother as reasons for his drug use".
Flowers was fined £400 and ordered to pay £125 in costs.
After his arrest, he said he did not think he was qualified to run a bank and admitted that he had "sinned".
He told BBC 2's Newsnight in March 2014: "I am in company with every other human being for having my frailties and some of my fragilities exposed.
"Most people get through their life without that ever coming into the public domain. I am no worse and no better it seems to be than any number of other people.
"But, of course, I have sinned in that old fashioned term, which I would rarely use, but I am like everybody else, I am frail."
