Edgar Da Silva opened the scoring after 17 minutes but the points were not made safe until the dying seconds when Rashid Hassan netted.
The win lifts Al-Shabab within touching distance of leaders Al-Ahly, with third-placed Al-Nasr now six points adrift of the top two.
Al-Jazira moved into fourth spot with a 1-0 victory over Al-Emirates, Ricardo Oliveira scoring the only goal six minutes before the interval.
Ajman let slip a two-goal lead as they played out a 2-2 draw at home to Al Wahda.
Ismail Matar (four) and Abdulla Al-Saadi (51) put the hosts in the driving seat but Al Wahda hit back with strikes from Simon Feindouno (55) Haddaf Abdulla (72).
Two goals from Makhete Diop helped Al-Dhafra on their way to a 3-2 win over Dubai SC.
The home side trailed after 10 minutes to a Malallah Ahmed own goal but Diop levelled the scores on the half hour.
Faisal Ali gave Dubai the edge once more after 55 minutes, only for Diop to register his second nine minutes later and Malallah Ahmed's own goal soon after settled the contest.