The 24-year-old striker took his tally to eight goals for the season on Sunday as Al Jazira opened up a one-point advantage over Al Ain, although the latter have two games in hand.
Mabkhout opened the scoring after 20 minutes and saw team-mate Manuel Lanzini double their lead six minutes later.
However, Al Shabab came storming back into the match and were ahead by the hour mark thanks to Azizbek Haydarov and a Henrique Luvannor double.
With a second successive defeat staring Al Jazira in the face, Mabkhout came to the rescue, with the winning goal coming three minutes into stoppage time.
Defeat drops Al Shabab down to fourth, with Al Ain also surging up the league after their 3-0 victory over Bani Yas, with star striker Asamoah Gyan netting twice.
Ten-man Al Wahda missed the chance to go top losing 2-1 to Al Ahli.
Following Adil Hermach's 10th-minute dismissal, Al Wahda quickly found themselves a goal behind as well, but rallied to go in level at the break thanks to Damian Diaz's penalty. However, Ismail Al Hammadi earned Al Ahli the win after 64 minutes.
At the other end of the table, Al Ittihad Kalba finally collected their first win of the season by beating Al Nasr 2-0.
The bottom-placed club struck twice in the closing minutes through Luis Leal and Wael Ayan and even Khamis Ahmed Mohamed's sending off could not dampen their celebrations.
Fellow strugglers Ajman also picked up three points with a 2-0 win over Emirates, meaning Al Fujairah dropped into the bottom two after a 3-1 defeat to Al Wasl.
Meanwhile, Al Dhafra put a three-point cushion between themselves and the bottom two with a 1-0 win over Al Sharjah.
