St Mirren say they were promised the West Stand tickets - priced £20 and £10 - once they had sold out their initial 14,000 allocation for the Scottish Communities League Cup final on March 17.
Instead they have been given an additional 1,200 tickets for the South Stand which cost £30 with no concessions, with the option for a further 900.
The Paisley club released a statement on Sunday saying the decision was especially disappointing "when we understand that Hearts have not yet sold their full allocation of 25,000 tickets".
The club added: "The decision was made to allocate the full 3,500 to Hearts without our knowledge. This information was only found out when we updated the SFL that we had just 100 tickets left late on Friday afternoon.
"We feel strongly that any decision on these tickets should have been delayed until closer to the final."
Saints apologised to their support and promised special deals for their upcoming Clydesdale Bank Premier League match against Celtic for any fans buying final tickets from now on.