Ballinderry will be appealing the straight red card for former Derry defender Kevin McGuckin ahead of their Ulster final against Glenswilly.
McGuckin appeared to be harshly sent off by referee Martin Higgins, on the advice of Cavan linesman Noel Mooney, for striking Kilcoo's Ryan Johnston after 22 minutes at the Athletic Grounds.
Both sides finished the game with 13 men. Ryan Scott of Ballinderry received a second yellow card 11 minutes into the second half, with Kilcoo having Johnston sent off for a second yellow in the last minute followed by a straight red for their midfielder Paul Greenan.
Ballinderry raced into a 1-5 to 0-1 lead after 18 minutes, with Collie Devlin and Conleith Gilligan punching serious holes in the Kilcoo defence.
Darragh O'Hanlon scored a free for Kilcoo in the third minute but the Derry champions hit an unanswered 1-5, including two eye-catching points from difficult angles by Ryan Bell.
Ballinderry could have had three goals in the first 10 minutes before Michael McIver finally hit the net after 14 minutes. McIver and Daniel McKinless both missed gilt-edged chances before the pair combined for the goal. McIver was put clean through and rounded the 'keeper to tap into an empty net.
Kilcoo, perhaps tired after two titanic extra-time battles with Crossmaglen in the last two weeks, chased shadows.
The Derry men were five points ahead when McGuckin was sent off, and their manager Martin McKinless confirmed they would be appealing.
"It's not often I slate referees but linesmen and referees have to take a hard look at it as these decisions change games. Those decisions were very rash. Kevin never touched him and they (Ulster Council) have to take a hard look at it."
Kilcoo trailed by 1-6 to 0-4 at half-time. When Scott received his marching orders Ballinderry were down to 13 men and struggling to get out of their own half as Kilcoo sensed an opportunity.
Enda Muldoon came on and won some vital primary possession, while Gareth McKinless and Darren Lawn carried a lot of ball and had fine games.
With all 13 remaining Ballinderry players inside their own '45' in the closing minutes, Kilcoo persisted in trying to engineer a goal when they should have taken points when they presented themselves.
They lost their discipline with time almost up, with the dismissals of Johnston and Greenan, and Michael McIver got the insurance point right at the death, to put them through to their first Ulster final since 2008.
Kilcoo manager Jim McCorry accepted that fatigue may have been a factor.
"No excuses, the best team won on the day," he said. "They got off to a blistering start and we were caught flat. I don't know if it was the legs or not. Maybe two titanic tussles like that with extra-time does take its toll."
Ballinderry, the 2002 All-Ireland club champions, will be hot favourites to beat first-time Ulster finalists Glenswilly in the provincial decider.
"There were a lot of celebrations out there, but we have won nothing yet," warned boss McKinless.
Scorers – Ballinderry: M McIver 1-2, C Devlin 0-3 (3fs), C Gilligan, R Bell 0-2 each, D McGuckin 0-1. Kilcoo: D O'Hanlon 0-3 (3fs), P Devlin 0-2 (1f), S O'Hanlon, C Laverty, S Devlin, J Johnston 0-1 each
BALLINDERRY – M Conlan; R Scott, C Nevin, M McIver; R Wilson, G McKinless, D Lawn; K McGuckin, J Conway; D McKinless, KM McGuckin, D McGuckin; C Devlin, R Bell, C Gilligan. Subs: D Conway for KM McGuckin (37), E Muldoon for Gilligan (53), A Devlin for D McKinless (57), F Bell for D McGuckin (57), P Crozier for Wilson (60).
KILCOO – S Kane; N Branagan, N McEvoy, D Branagan; D O'Hanlon, S O'Hanlon, Gerard McEvoy; P Greenan, A Branagan; P Devlin, N Morgan, R Johnston; J McClean, C Laverty, Gary McEvoy. Subs: J Johnston for Morgan (h-t), S Devlin for McClean (40)
REF – M Higgins (Fermanagh)