Johnston's goal put Kilcoo 1-6 to 0-6 up early in the second half and was always likely to prove decisive in such a low-scoring contest.
Kilcoo's lead was cut to a point but the Down champions moved three ahead again and then held on.
Scotstown duo Francis Caulfield and sub Brian McGinnity were sent off late on.
Caulfield was dismissed after getting a second yellow card while McGinnity saw red after appearing to strike impressive Kilcoo full-back Darragh O'Hanlon.
The Monaghan champions, beaten by Crossmaglen after extra-time in last year's provincial final, only had points from Darren Hughes and Donal Morgan to show for their early domination as several other good chances were missed.
Kilcoo hit back with five unanswered points after Aaron Branigan opened up their account in the ninth minute.
Conor Laverty's typically busy display was crucial to Kilcoo's improvement as Donal Kane, Paul Devlin (two) and Martin Devlin also notched points.
After being held scoreless for almost 20 minutes, Scotstown found their range again late in the first half as the lively Shane Carey pointed a free and keeper Rory Beggan also hit the target from a 45 after missing three earlier long-range efforts.
Aidan Branigan's departure at half-time looked a blow for Kilcoo but instead his replacement Johnston went on to become the central personality in the match.
The sides were level at 0-6 a piece when Johnston held his nerve to produce a great finish past Beggan after Laverty had flicked on a long ball.
After Shane Carey's reply, Johnston looked to have palmed in a second Kilcoo goal but the effort was ruled out - harshly it appeared - for a square ball.
The controversial decision looked as though it could be match-turning as another Carey point cut Kilcoo's lead to the minimum but crucially Beggan and Carey then missed chances to get Scotstown on terms.
Paul Devlin's superb long-range point and an Aaron Morgan score, after more great work by Laverty, left Kilcoo three ahead with three minutes of normal time left and Carey's seventh point was all Scotstown could summon in the remaining eight minutes of action.
In addition to Johnston and Laverty, Niall Branigan and Darragh O'Hanlon were among Kilcoo's stars as they set up a meeting either Kilcar or Glenswilly on 30 October.
Ryan Johnston's half-time introduction help Kilcoo edge out 13-man Scotstown 1-8 to 0-9 in the Ulster Club Football preliminary round game at Clones.