Fraser Anderson and Ross Cunningham were asked to play as wing backs, with manager Barry Cockburn opting to start with three at the back.
Unfortunately, the visitors made the most of that disruption in the United ranks and the men in green and white dominated proceedings throughout the first half.
Jake Grady did get behind the Thornton rear-guard on one occasion early in the match but his cross was cleared and the action quickly moved towards the other end of the park.
Kieran Dall missed a great chance at the back post before veteran Garry Thomson hit a couple of shots narrowly wide.
Hibs then took a deserved lead in the 25th minute when Nik Rendall could only clear as far as Andrew Adam and the midfielder lifted the ball over the advancing Kyle Moran to make the score 1-0.
Thomson and Jordan Lamont went on to test Moran with further efforts as half-time approached, yet St Andrews United gradually grew into the contest.
The impressive Lewis Sawers earned two free kicks that came to nothing and Grady was denied by a header off the line as well as a late offside call from referee Dickson.
Grady forced Thornton goalkeeper Ryan Linton into making a smart save at the front post in the first minute of the second-half but the visitors grabbed a crucial send goal moments later.
The Hibs players did well to work the ball down the left wing and Thomson managed to find the net from a tight angle in front of the changing pavilion.
The boys in the home side consequently suffered a dip in confidence for a spell thereafter and their opponents created a string of chances as a result.
Rendall headed a shot from Joe Kinninmonth off his own line, Dall hit the post, Thomson clipped the bar and Moran made two good saves from close-range.
St Andrews United boss Barry Cockburn, who was operating without his usual assistant coaches in attendance, switched formations to 4-4-2 and his team performed much better towards the end of the game.
Grady missed two half chances as Saints struggled to break down a well-organised Thornton defence and the last action of the afternoon resulted in Callum Macaulay receiving a yellow card for a frustrated challenge on substitute Jamie McNeish.
Saturday’s defeat saw Thornton, who sit one place behind Saints in eleventh position in the East of Scotland Football League’s First Division Conference A, make up some ground on the tenth placed north east Fife side.
Despite the weekend’s loss there remains plenty of optimism that Cockburn’s side can continue to climb the division in the weeks ahead.
This weekend sees United make the journey over the Forth to face Dalkeith Thistle.
Thistle may sit a couple of places below Saints in the league, but they have the luxury of six games in hand over Cockburn’s side.