Johnston, whose side stormed to the Division Two title and beat Rangers on their way to lifting the Ramsdens Cup, has been named alongside Neil Lennon, Stuart McCall and Terry Butcher.
Lennon steered Celtic to a second successive SPL title while the Glasgow side also reached the knockout stages of the Champions League and the Scottish Cup final.
McCall's Motherwell side are already guaranteed a Europa League place and look certain to finish second behind the Hoops this season.
Inverness currently lie in third place under Butcher's guidance and finished in the top six for the first time in the club's history.
PFA Scotland chief executive Fraser Wishart said: "This is the closest-run contest we have ever had.
"It speaks volumes for the quality of managers we have in our game in Scotland and there are a few more managers who I am sure could also lay claim to the title.
"All four nominees have had outstanding seasons and thoroughly deserve the accolade of being voted the best by their peers."