Doncaster and former Scottish Football League chief executive David Longmuir were the only two people in the running for the role following the merger of Scotland's two professional leagues.
A statement read: "The remuneration and appointment committee of the SPFL can advise that Neil Doncaster has been appointed to the role of chief executive officer of the SPFL.The SPFL looks forward to continuing with the implementation of one representative body and the commencement of season 2013/14 for the benefit of all 42 member clubs."
The panel was reported to be made up of Aberdeen chief executive Duncan Fraser, Celtic director Eric Riley, former Scottish Premier League chairman Ralph Topping and Stenhousemuir director Bill Darroch.
Doncaster appeared to be the clear favourite after the merger agreement was held up last week partly by the emergence of an outstanding £100,000 bonus for Longmuir, of which some SFL board members were unaware.
The limited selection pool has been widely criticised but it is believed that considering a fresh candidate could have fallen foul of employment law.
Doncaster's most important and pressing task is to secure a sponsor for the new league with the season starting four weeks on Saturday.