Club shareholder David Morris and John McFarlane were found not guilty of conspiracy to blackmail, false imprisonment and gun possession.
Blackfriars Crown Court had heard allegations Gianni Paladini was punched and threatened after an ambush by Mr Morris and a gang.
Jurors resume deliberations on charges against four others on Thursday.
Mr Paladini, 60, told the court he was forced to sign a resignation letter after being ambushed at gunpoint just before a home match in August 2005.
Mr Morris, 50, from Buckinghamshire and Mr McFarlane, 39, from west London, had denied all charges.
Outside the court, Mr Morris said he was happy the jury had reached "true and just verdicts of not guilty".