Thornton came from behind to take all three points in Craig Gilbert's 200th league game in charge of the team.
Sean McVicar put The Pansies ahead in the 5th minute with a well-placed shot from outside the box but the Hibs fought back and Garry Thomson capitalised on poor defending to stab home the 17th minute equaliser.
Chris Ireland saw his free-kick deflect off the defensive wall and hit the top of the crossbar and then Thomson watched in anguish as his free-kick also hit the bar to leave the half-time scoreline all-square.
After Thornton's trialist 'keeper made a terrific point blank save early in the second-half to deny Nathan Degernier, play switched to the other end where Lea Schiavone struck a powerful low shot into the Violet net to put Thornton in front.
Lee Milton came close to levelling affairs with a cross from the right which skiffed off the face of the bar, but the only other goal came in the 80th minute from Raymond Crichton who bravely headed home after Schiavone's free-kick took another deflection off the wall.
Window Store Hibs' Man of the Match – Stuart Drummond
Dundee Violet: Chalmers, Mudie, Henderson, Szpak, Degernier, Hood, Milton, O'Connor, Scott, Dignan, McVicar. Subs: Batchelor, Farquharson, Munro.
Referee: Mr G.Farmer
Match statistics:
Attempts at goal - TH 14 DV 7
Attempts on target - TH 4 DV 5
Corners - TH 6 DV 9
Fouls committed - TH 13 DV 22
Yellow Cards - TH 1 DV 3
Red Cards - TH 0 DV 0