Jamie Stephens was back in the Bees goal having recovered from injury, while Nugent handed first start to young Shane Cojocarel.
The first half didn’t play well for Barnet with the Bees lacking creativity across the pitch.
Jamal Campbell-Ryce took the ball to Cheltenham when he could, leaving their defence shaken from his pace.
John Akinde had two early half chances, but neither really tested Scott Brown in the Cheltenham goal.
The Bees tried to create, with David Tutonda driving forward when he could.
Jamie Stephens was called on after 9 minutes, saving from Carl Winchester to keep the score at 0-0.
But on 15 minutes a Bees defensive mix up saw Cheltenham’s Danny Wright latch on to a stray ball to slot past Stephens from 10 yards.
Things went from bad to worse when Shane Cojocarel went down in the area and had to be taken off with a suspected broken arm.
From there the Bees’ heads seemed to drop and they lacked energy in all areas.
A half chance for Akinola on 6 yards following Akinde’s pull back was all they could muster.
Akinde did what he could to chase down long balls, but the Bees seemed to lack answers in the final third.
Stephens was called into action again on 38 minutes, denying Liam Davis from 8 yards to keep Barnet in the game.
Tin Plavotic’s free header gave the Bees defence a scare from a corner a minute later, as Cheltenham pressed.
Luke Coulson broke into the Cheltenham area on the stroke of half time, but his cross was easily collected by keeper Brown.
The Bees went into the break needing a fresh energy, and thankfully they got it.
They came out in the second half looking more composed.
Other then a Carl Winchester free kick hitting the Barnet crossbar, the Bees weren’t really tested.
Curtis Weston joined the action on 55 minutes, replacing Tom Champion and that would prove to be crucial.
On 70 minutes Weston was there to riffle home from the edge of the box following Akinola’s knock down to pull the Bees level.
The game kicked on from there, when Charlie Clough’s header from a corner was turned in by John Akinde from close range on 76 minutes to put the Bees in the lead.
Less then two minutes later, Akinde was at it again when he found himself one on one with Cheltenham’s Brown to slot home Barnet’s third of the afternoon and complete a fantastic come back for the Bees.
A late penalty appeal from Amaluzor was the last of the real action, as the Bees played it safe to see out the victory.
Nugent had master minded a fantastic second half performance, and his first victory in the Barnet dugout.
At full time the players huddled together in the centre circle, showing their solidarity following a tough few weeks of results.
Full Time: Barnet 3-1 Cheltenham Town