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.

More than 5,500 people signed a petition against plans to build a five-metre embankment along the waterfront.
However, the council has admitted that there will never be a consensus on any flood protection proposal.
A report to a meeting of Dumfries and Galloway Council's environment committee next week will attempt to find a way forward.
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Chairman Colin Smyth said: "What we are now able to do is focus on what I think is the biggest issue as far as the public is concerned. In the draft proposal, the height of the embankment and the walls were simply too high and the public did not support that.
"What we now need to do is make sure that we find a solution that deals with the flooding, regenerates the Whitesands, solves the car parking issues, but also reduces the height of any proposed flood protection scheme."
Water from the River Nith regularly spills over into the Whitesands, flooding a major town centre car park and nearby business premises.
Campaigners against the Â£15m proposal to build an embankment claimed it would have a detrimental effect on the town's main beauty spots.
They also raised concerns that the move would lead to the loss of about 200 waterfront car parking spaces.
David Slater, a local businessman who has been one of the project's most vocal objectors, said: "However many other consultations they do now, public opinion will not change at this stage.
"It will be interesting to see how they can agree with the public to reduce the height of the bunds. There has to be better ideas because we can't put that in our town."
Earlier this year MSPs called for the row over the flood protection plans to be brought to a "positive conclusion".
The owners of Blackpool FC have lost a multi-million pound court battle with a Latvian investor.
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Senior councillors in Dumfries have pledged to find a compromise solution to the Whitesands flooding problem.