Jon Parkin's 42nd-minute opener put Ferguson's side ahead but midfielder McGugan struck twice in the final quarter to condemn Preston to a fifth defeat in six games.
The result served as another damaging blow to Ferguson after his side had lost 4-3 at Burnley on Saturday in dramatic fashion despite leading 3-1 with six minutes remaining.
Ferguson struggled to contain his anger with referee Kevin Friend at Turf Moor and was today charged by the Football Association with improper conduct for his behaviour towards the Leicestershire official.
And after the highly-rated McGugan stole centre stage, the Forest fans were left singing 'you're getting sacked in the morning' to a stunned Ferguson, whose side were booed off at the final whistle.
McGugan, outstanding throughout for Forest, found the space to unleash a fine shot from distance in the 11th minute which Preston goalkeeper Andy Lonergan parried clear.
The pendulum swing in the home side's favour moments later when Paul Coutts tried his luck from long range but Forest goalkeeper Lee Camp was equal to it.
In the 18th minute Forest carved out a fine opening which should have produced the game's opening goal.
Dexter Blackstock escaped down the right flank and flighted in a teasing cross which the unmarked Nathan Tyson somehow headed wide from inside the six-yard box.
Chris Gunter went close for Forest in the 37th minute when he blazed wildly over the crossbar when well placed and his profligacy was punished when Parkin struck five minutes later.
Forest surrendered possession midway inside their own half and Paul Parry's quick pass found Parkin lurking inside the 18-yard box.
The man nicknamed 'The Beast' showed a deft touch by collecting possession and holding off Gunter before drilling a low left-foot shot into the bottom corner.
It was his second goal in as many games and gave Preston a platform on which to build.
Yet Forest's threat as an attacking force steadily grew as the second half wore on and they were level in the 68th minute.
Tyson found McGugan inside the right channel and the midfielder turned and drove a low left-foot shot from over 20 yards out which deceived Lonergan and flew into the net.
Forest continued to probe and began pouring forward in greater numbers, so it was no real surprise when they grabbed the winner in the 81st minute.
A superb low, left-wing cross by Chris Cohen was met by McGugan, who smashed an unstoppable left-foot shot into the top corner from six yards out.