The Englishman, who was chief executive of the Scottish Premier League, has beaten off the challenge of Scottish Football League counterpart David Longmuir to lead the new 42-club organisation.
Both men were interviewed by a three-man panel at Hampden Park on Wednesday, which was reported to be Aberdeen chief executive Duncan Fraser, Celtic director Eric Riley, former Scottish Premier League chairman Ralph Topping and Stenhousemuir director Bill Darroch.
An SPFL 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."
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 pressing task is to secure a sponsor for the new league, with the season starting on August 3.