It will be another long week for Glory coach Kenny Lowe as more pressure mounts on his job as the head coach.
It was a great start for the Phoenix with debutant Sarpreet Singh getting his first goal with his first touch in the A-League, to put the home side 1-0 up.
Glory had some opportunities through a few set-piece free kicks from Diego Castro, with the first shot failing to trouble Tando Velaphi.
The Spaniard hit the second set-piece free kick beautifully, and a rare Andrew Durante reflection equalised the game before the end of the first half.
Glory pressed late in the game and got a penalty late through Diego Castro from a foul in the box, who easily became the villain after chipping the ball into the bread basket of Velaphi.
Six minutes later Roy Krishna scored the winner right on added time, and Phoenix held on to take the three points home for their fourth win of the season.
Next week Wellington head up to Gosford to take on bottom placed Mariners, meanwhile Glory play hosts to Melbourne City and a long week for Lowe.