Hunt was only on the pitch for a matter of seconds when he beat Blues keeper Boaz Myhill with a near-post tap-in to inflict on Chris Hughton's visitors their first defeat since September 18.
In a lively and entertaining contest, both goalkeepers were in sensational form.
A first half filled with chances and half-chances saw Myhill deny Kaspars Gorkss and Joseph Mills, while Adam Federici in the hosts' goal continuously frustrating Birmingham striker Chris Wood.
After half-time Reading winger Jobi McAnuff was superbly foiled by Myhill and the Royals' centre-back Alex Pearce saw a clearing header come back off his own post, before Hunt popped up to steal all three points for the home side.
Reading were the faster out of the traps, and Myhill in the Birmingham goal did well to tip centre-back Gorkss' goalbound header over the crossbar.
Moments later, the Latvian had another glorious chance to hand the Royals the early lead, but he could only stab the ball back across goal at the back post rather than working Myhill.
As if jolted into action by their hosts' early chances, Birmingham responded in kind on the quarter-hour.
Wood, on loan from West Brom, saw his fizzing shot kept out of the back of the net by the fingertips of Federici.
The breathless first half continued with home winger Jimmy Kebe breaking beyond the Blues' backline, only to see his pull-back from the byline fail to find a single Royals shirt in the six-yard box.
Wood nodded over for Birmingham at the other end, while the New Zealander then saw another shot stopped by Australian Federici low down before the home keeper continued his personal battle with the visiting centre-forward with a superb save to deny Wood's header.
After 20 minutes without a chance of any real significance, Reading were within inches of opening the scoring with 15 minutes left before the break.
Full-back Mills bombed forward out of defence and unleashed a curling, dipping effort from 20 yards which was turned over by Myhill.
And Reading captain McAnuff went agonisingly close to breaking the deadlock in the run-up to half time, narrowly missing the target with a header from Kebe's teasing cross with Myhill well and truly beaten.
But the Berkshire outfit had played out 14 goalless first halves prior to this fixture, and therefore it came as little surprise that the two teams went into the break level at 0-0.
When the game resumed the action was still being played out at breakneck speed, although chances were more scarce in the first 20 minutes of the second period.
Simon Church, restored to the Reading side in the place of Mathieu Manset, failed to test Myhill with a header before Chris Burke sent a savage 30-yard attempt over the crossbar for the visitors.
McAnuff had a huge opportunity to hand the Royals the lead when he seized on a weak Birmingham back-pass and bore down on goal, only for the inspired Myhill to parry his effort.
And the home skipper was almost made to rue the miss, as Birmingham struck the woodwork seconds later.
Reading defender Pearce miscued a clearing header which cannoned back off his own post.
After surviving that brief scare, however, the home side finally found a way past Myhill.
Noel Hunt, who had only been on the pitch a matter of seconds a substitute for Simon Church, tapped McAnuff's cross home at the near post.
It was the first goal Birmingham had conceded for exactly 500 minutes, and it left Reading with 15 more to hold on.
And that is exactly what they did.