At a convention in Donegal Town on Sunday evening the Laghey resident came out ahead of three other candidates.
At one point it looked as though Mr McEniff's daughter Elizabeth McIntyre would go forward uncontested but in recent weeks it became clear the position would be contested.
As well as Michael Naughton, former Ballyshannon Town Councillor Billy Grimes and Roger Meehan from Dunkineely threw their hats into the ring.
The seat became available when Mr McEniff, who was Ireland's longest serving Councillor, passed away in April
Michael Naughton is the manager of the Clanree hotel in Letterkenny and is also the manager of the Donegal ladies football team. He will officially take his seat at the next sitting of Donegal County Council