An uninspiring opening 45 minutes ended evenly, and it looked like both sides had settled for a point until Lions captain Jake Cooper leapt at the far post and looped a header over Pilgrims goalkeeper Michael Cooper.
The result leaves the Pilgrims in 21st, one point clear of Birmingham City in 22nd ahead of their season-defining clash against Hull City at Home Park.
In contrast, Millwall are safe in 16th place ahead of their final match against Swansea and can look forward to another season in the second tier.
“It is another mammoth game next week, we have been here before, we are going to need everybody on our side with us,” said Nancekivell.
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