The £1.75million dispute, centering on players who had been loaned to the club from Lithuanian side Kaunas, was revealed at the end of October.
Now they have come to an agreement to pay £1.5m in staged payments over a three-year period, starting in May 2013. A tax tribunal into the matter, due to begin next year, will now be scrapped.
The deal is separate to the settlement of a £450,000 bill yesterday which staved off the threat of a winding-up order.
Club director Sergejus Fedotovas said: "We are satisfied that this resolution provides the club with an opportunity to now move forward with certainty."