Morgan, who was loaned back to the Buddies after signing for Celtic in January, also set up the first goal as Saints got the win they wanted ahead of the Championship trophy presentation.
Morgan played in Danny Mullen to give St Mirren the lead in ten minutes.
Gary Oliver hit the bar in 18 minutes and Gary Harkins forced a great save out of Craig Samson in 29 minutes as Morton fought back.
And they found a leveller in 30 minutes when Michael Doyle powered a header into the net following a Frank Ross cross.
However, St Mirren won the derby in 73 minutes with a sweeping counter attack. Gavin Reilly stared it, found Cammy Smith who, in turn, picked out Morgan on the left side of the box and he slid a shot past Brennan.
Morgan was booked for goading the Morton fans but no-one in Paisley minded much.