Moret struck two minutes into stoppage time after being put through by man-of-the-match Tommy Leigh.
It was tough on Portland who had looked the better side for much of the game.
There was an early scare for Baffins when Jamie Symes saw his close-range shot deflect behind off the foot of goalkeeper Cameron Scott.
The Dorset side looked sharper and Jamie Beasley went close with a volley over the top.
Portland were adapting better on the difficult hard dust bowl of a pitch.
Baffins’ best chance came on 28 minutes after United goalkeeper Mike Edgar could only claw away a corner.
The ball fell invitingly to Parish in the area but the striker fired over the bar.
Baffins improved and went close as the interval approached.
A good move down the right ended with Robbie Taw slicing his shot narrowly over the angle of bar and post.
Both teams had half chances in a frenetic start to the second half.
Portland should have taken the lead when the unmarked Lewis Whyton headed wide from point blank range at a corner.
Baffins were living dangerously as Scott saved with his legs from Symes after the striker went clear.
Defences remained on top and clear chances remained scarce.
Then 15 minutes from the end Portland suffered a big blow when their goalkeeper was forced off following a collision with Parish.
Forward Darren Watts was forced to take over between the posts.
Deep in stoppage time Tommy Leigh threaded the ball through to Moret who fired into the far corner of the net to earn a fantastic win for Baffins Milton Rovers and crown their season in style.
Baffins Milton Rovers: Scott, Grimshaw, Williams, Wedlake, Burns, Cornish, Taw, T Leigh, Parish, Dart, Moret. Subs : Blakinson, Haley, McLean, A. Leigh, Tierney.