The Essex side were closing in on a sixth victory in seven league games under new manager Joe Dunne thanks to goals from Arsenal loanees Craig Eastmond and Sanchez Watt.
But then Hall, who only came on in 77th minute, powered home two headers in quick succession. Both came from Jon Taylor corners with Hall's equaliser coming eight minutes from the end of an exciting game.
Colchester, playing with plenty of confidence, were rewarded for a bright start in the third minute when Eastmond scored his second goal for the club. Eastmond tried his luck with a low, 20-yard shot which beat goalkeeper Chris Weale and went in the net off the inside of the far post.
Diminutive right winger Taylor was a constant menace as Shrewsbury responded well, but Colchester seemed set for another win when substitute Watt raced clear from the halfway line to rocket a shot into the top corner of the net from the edge of the box.
Shrewsbury were contemplating another damaging home defeat until Hall's intervention and they might even have won it late on had Taylor not blazed over from close range after fine work from Manchester City loanee Jeremy Helan.