Goals from Curtis Weston and Nicky Southall had earlier put the home side in control, but only a superb injury time save from goalkeeper Simon Royce ensured they left with a point.
Gills were humiliated 7-0 in the first meeting between the sides in September and began the game looking like a side determined to make amends. Weston gave them a dream start with a sublime volley from 20 yards after just three minutes.
It was a wonderful opening for the hosts, but they failed to build on the advantage in an otherwise poor first half. Shrewsbury, without an away win since August, stifled Gills with a 4-5-1 formation.
The visitors carried little attacking threat until first-half stoppage time, when Royce saved well from Ben Davies' deflected free-kick.
Gills appeared to have the points sewn up when they doubled their lead six minutes after the break. Kelvin Langmead was cheaply dispossessed by Simeon Jackson, whose impudent backheel allowed an unmarked Southall to slot past Luke Daniels.
With nothing to lose Shrews threw on Chris Humphrey and Moses Ashikodi, who both made an impact. The latter wasted a glorious chance when he slammed Holt's cross against the crossbar, but 12 minutes from time Ashikodi won a penalty when he tumbled following a shoulder charge from Barry Fuller.
It looked a soft decision, but Holt held his nerve to score from the spot.
The previously rock-steady home side suddenly looked fragile and three minutes from time Holt rose to head Humprhey's devilish cross home from close range.
The former Nottingham Forest striker almost completed a sensational hat-trick with an injury-time volley, but Royce somehow kept it out.