In their first competitive fixture for a month Colts co-managers James Orr and Craig McKinlay were forced into seven changes from the line-up from their win against Preston last month.
Spartans, impressive 4-0 winners at Broadwood earlier in the season, had most of the early possession.
But they failed to manage a shot on target while Colts squandered three good chances to take the lead.
FirstlyJamie Barclay ran forward from midfield to get on the end of a Stephen O’Neill pass and fire towards the top corner from 12 yards, but home ’keeper Blair Carswell dived full stretch to turn the ball around the post.
From the corner Blair Munn delivered a fine ball which led to a stramash inside the six-yard box, Andy Hunter, Michael Oliver and Barclay all trying to turn the ball home but seeing it blocked away by defence and ’keeper.
Spartans served notice of their own intentions as Dean Horribine sent a 20-yard shot whistling over the bar after a fine one-two with David Greenhill.
But Colts had another chance to score on the break as Munn delivered to the far post for Hunter who headed towards goal but saw his effort saved by the ’keeper.
Colts were punished for not taking their chances when Spartans scored the opener after a fine move.
Greenhill slid an inch perfect pass between the Colts centre backs for George Hunter to run onto and he confidently tucked the ball beyond Fahey.
Despite the setback the Colts continued to threaten their hosts and should have been level soon after when fine work between Hunter and Barclay set O’Neill free through on goal.
Colts’ top scorer looked set to make it 1-1 but Carswell managed to stop the ball low underneath his body.
Hunter forced the ’keeper into another save soon after as he got on the end of Robbie Duncan’s cushioned header to volley towards goal from 12 yards.
In contrast with the previous meeting between the sides, when Spartans were by far the better team, there wasn’t much between the sides - making the concession of a second goal two minutes before the break even more frustrating for the visitors.
From a Colts free-kick Munn swung in a fine ball which Scott Davidson turned back across goal, but the ball was gathered by Carswell who punted the ball 60 yards upfield.
Ross Gray flicked it on for Horribine, running from deep, and Fahey was left helpless as the Spartans man lofted the bouncing ball over his head into the net.
After the break the home side missed an early chance to make the game safe as slackness in the Colts backline saw Alan Brown round Fahey but take the ball too wide, only managing to find the side netting.
Jordan Pirrie replaced Munn after 60 minutes as the Broadwood men looked to find a way back into the game.
But in the early stages of the second half they struggled to trouble the Spartans keeper, the home side looking more likely without really testing Fahey in goal.
As the half wore on though it became clear it was going to be one of those days for the visitors as they hit the woodwork twice.
First Barclay got on the end of an O’Neill centre to head against the post from eight yards before O’Neill himself stepped inside two players on the Colts right before bending towards the top corner with his left foot, the keeper helpless as the ball hit the bar and went over.
Young Jeff Fergus replaced Kirwan, joining Pirrie to make two under-20s on the park and make his senior debut for the club.
Spartans added a third in stoppage time. Fahey skipped past the onrushing striker from a back pass from Oliver and looked to have been fouled.
But the official waved play on leaving Horribine to finish over Oliver’s head into the empty net.
Colts return to Ainslie Park again this Saturday to take on Spartans in the South of Scotland Cup third round.