The victory was no more than the hosts deserved after dominating the second half, but it was cruel blow for the relegation-haunted Harriers who had led since the 11th minute when Ian Foster netted.
After that the visitors defended doggedly and for a while it looked as if they might hang on to record only their second away success of the season - coming just five days after their victory at Oxford.
It had all started so brightly for Harriers as Foster cashed in on some shoddy defending by the home side and lifted the ball over advancing Lee Harrison.
Two minutes later they almost doubled their advantage when Dean Keates fired an effort against the upright and Blair Sturrock saw his follow up effort pushed away by Harrison.
The O's goalkeeper rescued his side again just before the break when he denied Sturrock once more following some dreadful defending.
All Orient had to offer in the first half was a free-kick from a Matthew Lockwood that goalkeeper John Danby saved comfortably.
But the second half was a different story as wind-assisted Orient battered the visitors.
Efe Echanomi and Scott went close before Daryl McMahon flashed a long-range drive inches over the top.
Orient's pressure finally paid dividends as Scott levelled with his seventh strike of the season firing home from the edge of the box after some good build up play on 74 minutes.
Orient continued to storm forward and Dan Chillingworth was denied by Danby before the home side grabbed the all important winner six minutes from time.
Orient, who had forced 12 corners, finally gained their reward when Alan White headed down Lockwood's flag kick and Scott crashed the ball home from 12 yards.