Riffa, who are based in Bahrain, looked to be in complete control in the first half and even went 1-0 ahead in the 27th minute thanks to Abdallah Deeb.
However, the three-time champions came roaring back in the second half as they outclassed Riffa in all departments.
Kuwait SC were finally rewarded for their hard work when Al Sanea levelled the score in the 51st minute.
But, Kuwait SC had to wait until the 73rd minute to go 2-1 up when Al Buraiki slotted the ball into the back of the net.
Despite the win, Ebrahim pointed out that his side were outplayed in the first half and were lucky to only concede one goal.
"Despite the win, I'm not satisfied with the performance in the first half while in the second period we were good in terms of performance and the result," Ebrahim told the-afc.com.
"The win will give us a big push for the next matches and I hope that the players will continue improving. The group is very hard as there are strong teams and it will be very hard to determine the teams that will advance from the group."
Riffa coach Branko Karacic was gutted to have lost since it leaves them in third place on the Group D points table.
To make matters worse, this was Riffa's second consecutive defeat in the 2015 AFC Cup after they lost 1-0 to Al Jaish of Syria on February 25.
"We had the upper hand in the first half but things changed in the second period and this affected us at the end," Karacic said. "Our players were tired in the second half and this affected our defence as we made some mistakes that gave the chance to Kuwait SC to get back into the match."