Kilmarnock had been holding out for a £2million package, and had already rejected four offers from Rangers in the close-season.
Rangers boss Walter Smith had claimed the loan signing of Amdy Faye from Charlton this morning was likely to be his last until January.
But the club revived their efforts to sign Naismith later in the day and the Scottish Football Association announced at midnight that the deal was done.
Sandy Bryson, head of the SFA's registration department, confirmed that paperwork confirming the deal was complete arrived by fax at Hampden at 11.59pm, beating the midnight deadline.