The Croatian striker joined 'Gers from Rapid for £4million, to be paid in instalments, in August 2010 but the financially-stricken Glasgow club have not been able to pay the full amount.
Rapid have accepted a payment of £717,000 - less than the £1.03m they were owed - for the 27-year old who left Ibrox for Everton in January 2012.
"We received the money from the 'new' Rangers yesterday (Tuesday) and the matter with them is closed," a Rapid spokesperson told STV.
"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."