The Syrian league champions were leading through a 15th minute goal by Aatef Jenyat when trouble erupted with seven minutes remaining after Mesaed Neda missed a penalty for the Kuwaiti side.
A smoke bomb was thrown towards the Al Karama bench and spectators rained missiles onto the match, forcing referee Yuichi Nishimura to stop the game.
The game was eventually resumed after a delay of more than 20 minutes but the hosts were enable to find an equalizer as Neda rattled the crossbar with a free kick.
The Kuwaiti champions were in the box seat coming into the match after holding to the Syrians to a goalless draw in the first leg and coach Mohammed Ibrahim made three changes to his squad with Saleh Al Hendi and Mohamed Mubarak making way for Abdulrahman Mussa and Bader Al Mutwa while defender Ali Al Shamali was ruled out due to injury and replaced by Abdulrahman Musaad.
Meanwhile, Al Karama coach Mohammed Kwid made only one change with striker Abdalrahman Akkari replacing defender Hassan Abbas.
Al Karama, who had made just the one change, dominated the opening exchanges and it paid dividends in the 15th minute with an excellent strike by Aatef Jenyat.
Midfielder Jehad Al Hussein cutting infield and feeding the ball to Jenyat 20 metres from goal, the 20-year-old blasting home past Qadisiya goalkeeper Nawaf Al Khaldi.
It brought the hosts to life as they now needed two goals to rescue their campaign.
Just four minutes Ivory Coast midfielder Ibrahima Keita should have leveled as he had a close range header saved by Al Karama goalkeeper Musab Balhous.
Good chances continued to go begging before the home fans, who had filled the stadium two hours before kick-off, were up to their feet on the 37th minute when Bader Al Mutwa went down in the penalty area but the referee Nishimura waved play on.
The Syrians should have sealed their passage to the final nine minutes into the second half when Mohammed Al Hamwi looped the ball over the crossbar after it was squared to him in the middle with the Al Qadisiya goalkeeper hopelessly out of position.
Searching for that elusive goal Ibrahim brought on three attacking players – Mohammed Mubarak, Saleh Al Hendi and Mohammed Rashed – and the moves nearly paid dividends as Al Qadisiya laid siege to the Al Karama goal, keeping Mosab Balhous extremely busy for the rest of the half.
After spurning many chances, Al Qadisiya were thrown a lifeline with seven minutes remaining when they were awarded a penalty after defender Fabio Santos handled the ball.
However Neda had a shocker as he blasted the ball well over the bar much to the outrage of the local fans.
In their frustration the Al Qadisiya fans hurled a smoke bomb at the Al Karama bench forcing their officials and players to run onto the pitch away from the thick smoke.
The game was stopped for over 20 minutes and only continued after Al Qadisiya officials forced the fans in the stand behind the Al Karama bench to leave the stadium.
In the remaining time, Al Karama could have doubled their advantage when Mohamad Al Hawmi broke clear but saw his low shot saved by Al Khaldi.
Neda then fired a free kick against the woodwork as the Kuwaiti side's dreams of reaching the final dissipated along with the remaining smoke.
Al Karama will meet Korean side Jeonbuk Hyundai Motors in the final with the first leg in Korea on November 1.