The heavily re-directedgoal gave the Lions the lead just after the half hour mark, Feeney’s effort taking a huge change of direction to wrong foot goalkeeper Steve Simonsen and end up in the back of the net.
It had been a game of few real chances to that point. Steve Simonsen had twice tipped away efforts from his near post from Shane Lowry and the dangerous Darius Henderson.
The best chance for the home side prior to the goal came when Henderson fired another shot that took a deflection off North End skipper John Mousinho and came back off the cross bar on 20 minutes.
The Lilywhites came into the game the more the half went on and with 24 minutes gone Shane Cansdell-Sherriff delivered a straight free kick into the penalty spot, which Jack King flicked on and centre half Paul Huntington smashed on the volley, unfortunately it was over David Forde’s bar.
Five minutes later and a great run from Stuart Beavon won PNE’s first corner, running off King’s flick on. Cansdell-Sherriff’s excekkent corner was tipped away by Forde.
However, shortly after the opening goal came. James Henry found space down the right and delivered into the box. The yellow FA Cup ball found its way out to Liam Feeney in the left hand corner of the penalty area, and his left foot effort took a huge deflection, taking what would have been an easy save by Simonsen, of Darius Henderson and up and over the keeper into the back of the net.
The goal didn’t take any wind out of North End’s sails, as on 36 minutes another good run from Beavon, from deep, saw the No.29 drive into the Millwall box, but he dragged a right foot effort wide of the left hand post.
North End made a double change at the break, manager Graham Westley putting Amoo and Byrom on for Kane and Cansdell-Sherriff, the formation becoming 4-3-3.
Steve Simonsen thwarted former team-mate Henderson with a strong hand after the Lions' No.7 had found space to shoot in a right hand channel.
Wroe then won a corner with a deflected effort just before the hour mark with North End on top in the opening stages of the second half.
At the mid way point in the half North End had two excellent free kick opportunities. The second of which was 20 yards out in a left hand channel. Nicky Wroe's shot was blocked, seemingly by a hand, but the refreee waved away calls for a penalty.
Graham Cummins replaced skipper John Mousinho with nine minutes left, the North End No.21 pulling up with what looked like a strain.
Stuart Beavon saw a shot deflected just wide with five minutes left with the Lilywhites throwing everything at the home side. Sub Cummins then had a shot blocked by Ireland keeper Forde, with Robertson flashing Beavon's corner wide.
Three mins were added on with North End pushing for a replay, but the home side held on to edge through to the fourth round.
PNE line-up: Simonsen, Mousinho (Cummins, 81), Cansdell-Sherriff (Byrom, 46), Welsh, Huntington, Robertson, Kane (Amoo, 46), Wroe, Beavon, King, Buchanan. Subs not used: Stuckmann, Procter, Beardsley, Hayhurst.
Millwall line-up: Forde, Wright, Henderson (J Smith, 87), Lowry, Henry, Feeney (Batt, 46), Beevers, N’Guessan, A Smith, Abdou, Osbourne. Subs not used: Taylor, Dunne, Racon, Marquis, Wilkinson.
Attendance: 5,364 (467 away fans)
Referee: Mr C Pawson