Sean Maguire and Brad Potts came into the side in place of Emil Riis and Ali McCann.
Riis was ruled out with a hamstring injury, while McCann dropped down to the bench after standing in for the ill Potts against Queens Park Rangers.
Maguire got the nod to start alongside Cameron Archer up front, having impressed as a substitute last week.
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It was his first start in the Championship since Lowe’s first game in charge against Barnsley in December.
There was a seat on the bench for Ched Evans after the striker missed the Blackpool and QPR games with a toe injury, with Josh Earl returning after a stomach bug.
But Mikey O’Neill missed on the matchday squad having made his debut as a late sub against QPR.
O’Neill played for the Under-19s in midweek and on Thursday had his contract ended – he’s also been offered a professional deal along with Aaron Bennett.
PNE: Iversen, Van den Berg, Bauer, Hughes, Whiteman, Potts, Browne, Johnson, Cunningham, Maguire, Archer. Subs: Ripley, Evans, McCann, Sinclair, Earl, Diaby, Murphy.
Millwall: Bialkowski, Ballard, Cooper, M Wallace, McNamara, Mitchell, Kieftenbeld, Malone, J Wallace, Burke, Afobe. Subs: Long, Hutchinson, Bradhsaw, Ojo, Saville, Leonard, Evans.
Referee: Thomas Bramall (Sheffield)