After a first half that remained goalless, despite countless chances, it was Garner who reacted with an instinctive touch in the penalty box for his tenth goal of the season.
A corner from Marc Bridge-Wilkinson was missed at the near post by a defender and, having escaped his marker, the £140,000 record signing stabbed the ball in from six yards.
In a thrilling first half, it was Bridge-Wilkinson who went closest to breaking the deadlock when his wicked curling free-kick struck the outside of the post.
But the diminutive player was then booked for a rash foul on Adam Chambers, before out-of-luck Carlisle striker Danny Carlton poked a volley into the side-netting.
Orient hit-man Jabo Ibehre should have netted after 33 minutes when he picked up Chambers' throughball and powered his way past the Carlisle defence but, with just keeper Keiren Westwood to beat he fluffed his lines, allowing the shot-stopper to palm the ball away.
Garner and Carlton both went close for the Cumbrians with Garner forcing Glenn Morris to make a great low save after turning smartly on the edge of the box.
Two minutes before the break, the visitors were left fuming when referee Scott Mathieson disallowed what appeared to be a perfectly good goal.
A deep cross was swung into the box and, with Westwood and Chambers challenging for the ball, John Melligan stole in to nod the ball over the line from close range.
Orient celebrated before realising that a free-kick had been given for a foul on Westwood.
Despite dominating possession after going a goal down, Orient failed to force Westwood to make a save and, although Adam Boyd nearly snatched a point with a dipping 40-yard volley in stoppage time, it was a deserved win for Carlisle.