Rapid have accepted a payment of 820,000 euros (£717,000), less than the 1.18m euros (£1.03m) they were owed by Rangers, according to the Scottish club's failed CVA in the summer.
Rangers chief executive Charles Green had agreed to pay all football debts from the liquidated oldco to clubs as part of the deal to have the club's membership of the Scottish FA transferred to the newco in July 2012.
A Rapid spokesperson told STV: "We received the money from the 'new' Rangers yesterday (Tuesday) and the matter with them is closed.
"We have assured them we will not raise any dispute with FIFA which could have potentially blocked their participation in future European competitions.
"We are still trying to recover the full amount from the 'old' Rangers, but we understand this may take many months."
Striker Jelavic, who now plays for Everton, joined Rangers from Rapid in the summer of 2010.
GAIS, Orebro and Palermo say that they have received negotiated amounts from Rangers over fees due for the transfers of Mervan Celik, Alejandro Bedoya and Dorin Goian respectively.
St Etienne reportedly declined to comment on whether they have been paid for money due for the sale of Carlos Bocanegra to Rangers in the summer of 2011.