Thornton got off to a bad start on Wednesday night and despite drawing level soon after, slack defending and the inability to convert chances were to cost them any chance of victory.
Bathgate went ahead in the 5th minute when Aiden McKee converted Robin Feeney's low cross from close range. This lead lasted just three minutes before Stuart Drummond lashed the ball high into the net to give the Hibs an equaliser.
Only another four minutes passed before Feeney put the visitors back in front and this completed the first-half scoring.
Early in the second-half, Ross Harkness made a good save to prevent Garry Thomson from levelling affairs and this save proved crucial because by the 51st minute it was 3-1 when Feeney beat the offside trap to shot the ball low into the net.
In the 56th minute Bathgate broke at speed, the end result being a goal from Stephen Easton but although a Stuart Drummond penalty strike in the 75th minute reduced the deficit to two, Thornton couldn't find the net again leaving Michael Wilson's team to travel back across the Forth with all three points.
GI Joinery Hibs' Man of the Match: Mikey Lee
Thornton Hibs: Linton, M.Robertson, McMillan, Shanks, Shields, A.Drummond, S.Drummond, Hepburn, Anthony, Thomson, Adam. Subs: Ireland, Lee, Coleman, Feeley, Roberts.
Bathgate Thistle: Harkness, John Henderson, Harris, Boyle, McCreadie, Macleod, Cormack, Feeney, McKee, Easton, Bonnar. Subs: Jack Henderson, Macmillan, McKeon, Wight
Referee: Mr S. Gill
Match statistics:
Attempts at goal - TH 24 BT 6
Attempts on target - TH 13 BT 4
Corners - TH 7 BT 3
Offside - TH 1 BT 1
Fouls committed - TH 12 BT 15
Yellow Cards - TH 1 BT 5
Red Cards - TH 0 BT 0