There was a seat on the bench for Bambo Diaby who on Monday signed a contract for the rest of the season, having trained with PNE since November.
Lowe had spoken on Monday about keeping the player fresh.
It was centre-half Lindsay's first appearance since the derby defeat at Blackburn Rovers on December 4.
Millwall: Bialkowski, Hutchinson, Cooper, M Wallace, McNamara, Kieftendbeld, Mitchell, Malone, Burke, Bennett, Afobe. Subs: Long, J Wallace, Pearce, Saville, Mahoney, Evans, Burey.
PNE: Iversen, Van den Berg, Lindsay, Hughes, Whiteman, Potts, McCann, Ledson, Cunningham, Riiis, Evans. Subs: Ripley, Earl, Diaby, Bauer, Browne, Archer, Sinclair.
Referee: Kevin Friend (Leicestershire)