Glazer owns 28.1% of the team which is valued at about $1.36 billion and ranked by many as the world's richest sports franchise.
"Manchester United supporters will take this as a declaration of war said Sean Bones vice chairman of the fan-based group Shareholders United.
Man United last month broke off talks with Glazer about a possible takeover calling his proposal "unattractive" because it relied too heavily on borrowed money. But the club has said it expected him to make another offer.
Irish racehorse owners John Magnier and J.P. McManus who own 29% of the club abstained from voting as has been their custom in recent years. Glazer voted through a representative.
If Glazer's ownership share reaches 30% British law requires him to make an offer to buy out remaining stockholders. Shareholders United urged fans to buy Man United shares with a goal of boosting individual fan ownership to 25%. Such a move would make it difficult for Glazer to assume control.
Opposition to a possible American takeover has been fierce. Fans oppose Glazer because he's a foreigner and they fear he will raise ticket prices and sell Old Trafford to increase club profits.
The ouster of board members Maurice Watkins Andy Anson and Philip Yea came as blow to chief executive David Gill who recommend the three for re-election. Man United said the vote by Glazer was the deciding factor in the rejection of the board members.
"Had the Glazer Family abstained or voted in favor of these resolutions they would all have been passed the team statement said. "The board are very disappointed with this outcome as we do not believe it is in the best interests of the company."
Old Trafford was packed with fans who spoke out against any takeover by Glazer. Shareholders United says it represents the views of small investors who make up about 18% of the club.
United has about 260 million shares outstanding with a vote awarded to each share. United said the three directors were voted off 74.3 million to 34.9 million.
Watkins was the most contentious board member up for re-election. Last month vandals splattered red paint on his house and cars after he sold 1 million shares to Glazer.