Short-staffed again, Hibs made their exit from the King Cup and played for 51 minutes with only t10 men following goalkeeper, Callum Doran's, dismissal.
By then the damage had been though as poor defending meant that the students were two up by the 13th minute with their captain, Gregor Macdonald, bagging a brace.
Alasdair Shrive's deflected shot made it three in the 31st minute and then came Doran's red-card after he brought down Russell Cairns just outside the box.
With no regular goalie on the bench, the unfortunate Daniel McNab was substituted by Andy Adam and the first thing the replacement keeper had to do was pick the ball out of the net following Charlie Stewart's low drive.
The closest Thornton came to finding the net in the first-half was when Joe Kinninmonth's strike was superbly tipped over by Alex McMahon in added time.
The second-half was always going to be about damage limitation for Craig Gilbert's men but they did come close to reducing the leeway twice.
First, Jamie McNeish raced from the half-way line and after going past McMahon, his shot from a very acute angle struck the upright as it flashed across the face of the goal.
Then Max Coleman's curling shot from the edge of the box also struck the post to sum up the Hibs' luck.
Thornton Hibs: Doran, Robertson, A.Drummond, Meldrum, Shanks, McMillan, McNeish, Coleman, S.Drummond, Kinninmonth, McNab.
Subs: Rolland, Adam.
Heriot-Watt University: McMahon, Hogg, Kerr, Wishart, Thomson, Shrive, McCreadie, Potter, Cairns, Macdonald, Stewart.
Subs: Chingwalu, Turnbull, Richmond, Robertson, Boyko.
Referee: Mr A.Budd.
This weekend Thornton return to league duty when they make the journey to face Leith Athletic.
Leith are amongst the First Division Conference A’s pace-setters and will be sure to offer a stern test to Thornton who go into the game sitting in sixth place.