The match saw both sides finish with ten men at the Limbe Stadium.
VAR intervened twice during the quarter-final match to ensure that Syli National midfielder Mory Kante and Rwanda goalkeeper Olivier Kwizera were sent off in separate incidents.
Guinea playmaker Morlaye Sylla scored from the resultantly free-kick in the 60th minute after Kwizera was penalised for his late tackle on advancing striker Yakhouba Barry.
The goal was enough to send Guinea to the last four of the tournament in the Central African country where they will face neighbours Mali on Wednesday.
Guinea suffered a big blow in the15th minute when captain and midfielder Mory Kante was sent off after VAR review after an incident in midfield.
The AS Kaloum player was shown the door for the serious tackle on captain Jacques Tuyisenge that led to the forced substitution of the Rwandan captain because of the resultant injury.
Injuries forced Rwanda to make two early substitutions as Tuyisenge left the pitch to be replaced by Sugira Ernest following the injury.
Martin Twizeyimana took the place of Rashid Kalisa on the half hour mark as he was also forced out of the game because of injury.
Guinea through into semis
Despite the early substitutions, the Amavubi made their numerical advantage count by pinning the Guineans on their side forcing goalkeeper Camara Moussa to come out to make some saves.
The West Africans also worked hard in defence following a flurry of attacks into their area while they relied on counter-attacks to punish the Rwandans.
Kwizera was sent off following intervention by the VAR as the Rwanda goalkeeper was found to have fouled by advancing tournament leading scorer Yakhouba Barry.
Playmaker Morlaye Sllya curled the resultant free-kick beyond substitute goalkeeper Yves Kimenyi on the hour mark to break the deadlock.
The result of the match means Guinea are through to the last four of the tournament designed exclusively for home-based players.
The semi-final will start on Wednesday when Guinea take on Mali at the Japoma Stadium in Douala.