The opening goal came after nineteen second when Mabkhout received a quality pass from Omar Abdulrahman to score his third goal of the tournament with a shot.
Bahrain pulled a goal back in the 26th minute when Jaycee scored with a header from a Faouzi Aaish corner.
With the match looking like it was heading for a draw, UAE took a surprise lead when Bahrain captain Mohamed Hussain headed the ball into his own net to hand the UAE the 2-1 win.
UAE are now assured of a quarter-finals spot, while Bahrain have recorded two straight losses.
The UAE top the group with six points and qualify for the last eight along with either Iran (3 points) or Qatar (0 points), depending on the outcome of their match on Thursday
UAE travels to Brisbane for the final match of Group C on Monday while Bahrain takes on Qatar in Sydney.