Owen and Karl Oyston, owner and chairman of the club, were in dispute with businessman Valeri Belokon.
The League Two club owners may have to pay out almost £3m ($3.75m) after a judge at Manchester Civil Justice Centre ruled in Mr Belokon's favour.
He invested £4.75m in 2008 to develop the club's South Stand and the dispute was over his share of profits from it.
A forensic accountant will work out the exact figure the Oystons have to pay at a later date, the hearing was told.
The final figure is believed to be between £1m and £2m plus £900,000 costs.
The Oystons and Mr Belokon disagreed over the income and profits generated following the development of the South Stand.
The row also centred on the deduction of legitimate expenditure, including a loss-making Blackpool hotel, from what Mr Belokon believed he was owed under the commercial agreement.
The three men involved were not present in court.
Eric Shannon, representing the club, applied for leave to take the case to the Court of Appeal, but this was refused by Judge Jane Moulder.
Thousands of fans have been boycotting their home games in protest at the ownership and running of the club by the Oyston family.
In January, fans staged a joint protest with Blackburn Rovers at their FA Cup clash.
The team has plunged down the Football League to the fourth tier just six years after being in the Premier League.
Mr Belokon bought shares in the club in 2006 and was heavily involved in their rise through the ranks culminated in promotion to the Premier League in 2010.
In a rare public appearance last July, Owen Oyston said the club was not for sale.
The owners of Blackpool FC have lost a multi-million pound court battle with a Latvian investor.