The summer signing rolled the ball into an empty net to seal the points for the home side in a game short on incident.
It was The Jags who created the game’s first chance when Lyle Taylor fired narrowly wide after Declan McDaid’s lay-off.
They continued to dominate with Christie Elliott heading over from Stephen O’Donnell’s cross, while Elliott went close a few minutes later with another header.
Thistle then had five corners in a row with Conrad Balatoni heading the last set-piece narrowly over.
The Dark Blues’ finally carved out an opportunity when Jim McAlister blasted the ball over the bar after Paul McGinn’s cross from the right flank.
On the stroke of half-time the home side tested keeper Scott Fox, who clawed away a free-kick from Alex Harris.
But Fox was forced to go off at half-time for Paul Gallacher after picking up an injury.
The second half was a tame affair with neither side at their best.
Dundee’s best chance fell to Paul Heffernan who fired an effort wide from inside the box, while at the other end Taylor could not get his shot on target from Gary Fraser’s cross.
The home side did put the ball in net on 67 minutes through Gary Harkins but he was flagged off-side.
The game looked to be petering out until Harkins jinked his way into the box and crossed for McGowan to net a dramatic winner.
Dundee are now up to sixth place in the table while Partick stay in ninth.
Partick have not won away from home since thumping Inverness 4-0 in December.