The game looked destined to end goalless after a turgid encounter in North London but, with just 20 minutes remaining, Furlong produced a moment of magic to break the deadlock.
Taking the ball with his back to goal, Furlong turned Ian Sharps exquisitely before rolling the ball past the exposed Andy Warrington to open the scoring.
And with just nine minutes remaining, the striker met Albert Adomah's right-wing cross with a thumping header to claim his eighth of the season and all three points.
In a dire first half, it was Barnet who looked the more likely to break the deadlock as Rotherham's long-ball tactics proved fruitless, with them aiming to equal a club record six successive away league wins.
The home side came closest to opening the scoring just after 20 minutes but John O'Flynn's far post header was brilliantly clawed away by Warrington.
But that was to be the Irishman's last contribution as he limped out of the action just minutes later after pulling up sharply with a hamstring problem.
Rotherham had won five of their previous away games before their trip to Underhill, but they looked off the pace as Barnet continued to dominate.
Buoyed by their fine win at Gillingham last weekend, Ian Hendon's men looked sharp and confident in possession against the South Yorkshire side.
But their failure to convert their dominance into goals almost cost them dear as Drewe Broughton burst through the Barnet back-line, only to be thwarted by Kenny Gillet's sliding tackle.
With the game beginning to open up, Rotherham started to look more threatening and Jake Cole did well to turn away Broughton's fierce drive following Mark Burchill's lung-busting run.
It was Barnet's turn to go close just seconds later as Yannick Bolasie's right-wing cross was flicked on by Furlong, but Adomah's rocket effort was beaten away by Warrington.
But there was nothing the Rotherham keep could do just minutes later as Furlong rolled the ball through the legs of Sharps and did the rest.
It was no less than Barnet deserved and Furlong sealed the points with nine minutes remaining.
Both Bolasie and Adomah went close as the Bees looked to add a third but it proved inconsequential as they completed a double over the Millers for the season.