Chiefs lost 3-0 on aggregate in the two-leg affair against their North African opponents.
The score on the night was still locked at 0-0, with Chiefs the dominant side when a mistake by defender Siboniso Gaxa gifted the hosts the goal that ended the tie as a contest.
With three minutes remaining, Gaxa failed to control the ball in his own area and was dispossessed by Raja striker Osaguona Ighodaro who easily deposited the ball into the back of the net to open the scoring.
Ighodaro scored again in injury time when another defensive error by Chiefs allowed the player to receive the ball unmarked, and from close range he made it 2-0 to inflict a harsh scoreline on the South African side.
The AmaKhosi had their chances on the night, but a lack of clinical finishing up front did not help their cause.
Without the services of influential midfield playmaker Siphiwe Tshabalala, Chiefs started the match on the back foot.
The home team began probing for an opener and spurned a great chance on the quarter hour mark. Yassine Salhi found his way in behind George Lebese in the Chiefs box, but the player opted to pass to a teammate and the ball drifted tamely to safety.
Eight minutes later Adil Karouchi for Raja sent in a looping ball into the six-yard area, but Chiefs shot-stopper Itumeleng Khune made a good acrobatic save to stamp out the danger.
After navigating the initial period of pressure applied by the hosts, Chiefs began to slowly work their way into the contest.
In the 25th minute, Lebese ran through one defender in the box but his shot from close range took a deflection off an opponent when it seemed certain he would open the scoring.
In first half injury time, Lebese ran into the Raja box and had the defence on the backfoot, but his cross could not find a teammate as the danger was cleared. It would be the last action of the opening period of play, sending the teams to the break goalless.
In the 48th minute, Lebese spurned one of the chances of the match. The Chiefs player received the ball on the edge of the area, and with just Raja keeper Hicham El Allouch to beat, Lebese bashed his attempt inexplicably wide of goals.
Mandla Masango had a dip at goal from long range in the 69th minute, but his volleyed attempt sailed over the crossbar.
The visitors kept on pushing forward and always looked like they would eventually break the deadlock, but the final pass was always lacking.
Then in the dying minutes, it was the turn of the hosts to make the double-strike and send Chiefs home empty-handed.
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