Long controlled Nicky Shorey's deep free-kick and lashed home to seal Reading the three points after Michael Duberry's own goal had seemed set to gift the visitors a point.
Dave Kitson's neat finish had put the home side in front after Reading striker Leroy Lita had wasted a hat-trick of chances in a goalless first half.
Kevin Doyle, who scored twice as a substitute in the defeat at Blackburn last week, was employed on the right of midfield as Royals boss Steve Coppell continued with a strike partnership of Lita and Kitson.
And it was Lita who gave Newcastle the most trouble as he looked lively on his first home Premier League start in eight weeks.
The England Under-21 striker had a glorious chance to open the scoring on ten minutes when Doyle got into space on the right and squeezed a low cross that was just behind the in-rushing Lita, leaving the striker embarrassed as the ball bounced against his standing foot.
At the other end, Michael Owen, who made his comeback from a knee injury in this fixture last season, looked to have been gifted the chance to open the scoring when Ibrahima Sonko allowed a speculative cross to drift beyond him and was grateful to see Graeme Murty and Marcus Hahnemann combine to scramble the ball away to safety.
Lita went close again when he showed great strength to hold off Claudio Cacapa but then sent a left-foot shot straight at Shay Given.
Newcastle could feel fortunate to be heading in on level terms at half-time, especially when Lita narrowly failed to turn the ball home at the far post after Stephen Hunt had flicked on following a great run and cross from Doyle.
But Reading did finally make the breakthrough eight minutes into the second half when Hunt and Lita combined to roll the ball into the path of Kitson, who showed great awareness to float a left-foot shot over the outstretched arms of the stranded Given.
But the visitors were level 14 minutes from time when Hunt fouled substitute James Milner and Emre's free-kick evaded Kitson before being bundled over his own line by the hapless Duberry.
Reading's response was a positive one and Long made an immediate impact seconds after replacing the tiring Lita.
The young Irish striker latched on to Sonko's flick-on from a Shorey free-kick and then rifled into the roof of Given's net to secure the home side a deserved victory.