The former Preston striker stole in at the near post to steer home Liam Lawrence's mishit shot midway through the second half after a spell of extended pressure.
Portsmouth's leveller was just reward for an impressive second half, having previously seen a Nugent goal ruled out for offside, with Dave Kitson also firing another chance agonisingly wide and Hayden Mullins hitting the upright.
Steve Cotterill's side, however, looked second best throughout the majority of the first half and deservedly went behind to a Liam Trotter header. Nugent, though, thwarted the Lions' hopes of securing their second victory at Fratton Park in 18 attempts and, in truth, they were lucky to escape with a point.
Portsmouth were boosted heading into the clash by the return of influential defender Hermann Hreidarsson, who made his first start in nine months after rupturing an Achilles tendon.
The visitors, meanwhile, handed the skipper's armband to Alan Dunne in Paul Robinson's absence. Like defensive partner Danny Shittu, he was struggling with a hamstring problem.
The match started frenetically on a bitter afternoon in Hampshire, with Portsmouth captain Aaron Mokoena lucky not to be sent off within 78 seconds for a lunge on Steve Morison.
Just two minutes later, the Londoners came agonisingly close to breaking the deadlock through on-loan Southampton winger Jason Puncheon, who followed up James Henry's parried effort.
The visitors' bright start continued and, after several clear-cut chances, Kenny Jackett's men netted a 26th-minute opener. Puncheon played a superb ball through to Morison, whose fierce shot was parried on to Trotter and his header floated into the top corner.
By this point, Millwall were looking particularly dangerous down the left flank, where Hreidarsson was enduring a torrid afternoon.
Morison twice came close to doubling the visitors' advantage as half-time approached, although their attacking onslaught could not muster a second goal. Portsmouth started the second half with renewed vigour and only a late block prevented Michael Brown netting an equaliser 16 seconds after the restart.
Two minutes later, Nugent wheeled off in celebration after slotting home a loose ball, but the Pompey chimes were short-lived as the goal was ruled out for offside.
The Londoners rode their luck as Kitson stabbed a shot agonisingly wide in the 56th minute, but Cotterill's men began to wane and Joel Ward was forced into a goal-line clearance five minutes later.
Mullins clipped the outside of the upright with a first-time shot in the 62nd minute and Portsmouth's equaliser eventually came 11 minutes later in somewhat fortuitous circumstances.
After Lawrence's corner was half-cleared, the midfielder mishit a shot that was going wide until Nugent stole in at the near post to head home.
Both sides pressed forward in search of an all-important winner but saw their attempts nullified by resolute defending at either end.
Portsmouth 1-1 Millwall: Match Report - view commentary, squad, and statictics of the game as it happened.