Wales striker Morison tucked away his 12th goal of the season to secure victory for the in-form Lions, who continue to close in on the play-off places.
Jewell, who was in the stands to watch the stunning midweek Carling Cup win over Arsenal, took charge of Town for the first time on Saturday and saw Wednesday's goal hero Tamas Priskin fire his new side ahead at the New Den.
But Millwall hit back before half-time through Danny Schofield and Morison made up for a dreadful first-half miss with the winner to extend their unbeaten league run to nine matches.
Jewell predictably named the same line-up which saw off the Gunners as he returned to the dug-out for the first time in more than two years.
But it was the hosts who came out of the blocks quicker with Morison shooting straight at Town keeper Marton Fulop and Alan Dunne firing wide.
However, Priskin made the breakthrough in the 25th minute for the visitors with a fine solo effort.
The Hungarian won a header from Carlos Edwards' cross and chased down the ball himself before coming up with a deft finish to beat home keeper David Forde.
Millwall attempted to hit back and Morison met Scott Barron's corner with a header which flew the wrong side of the post and into the side-netting.
Ipswich came close to doubling their advantage in the 37th minute but Jaime Peters' hopeful cross-shot came back off the crossbar and Priskin could not tuck away the rebound.
At the other end Morison burst through only to put his shot too close to Fulop and Neil Harris headed over.
The equaliser came a minute into first-half stoppage time when Forde's long clearance was headed into Schofield's path by Harris, and the winger drilled a first-time shot past Fulop from the edge of the area.
Morison passed up a gilt-edged chance on the stroke of half-time when Edwards' mistake let the striker in but he dragged his shot wide.
After the break Fulop did well to deny Morison again, prodding the ball away from the frontman without bringing him down.
But Morison made no mistake 14 minutes from time when he got to a cross from substitute Chris Hackett just before Fulop and tucked the ball into the net.
Ipswich almost grabbed a leveller at the death but Forde made a sharp save from Jason Scotland to secure the points.