Marc Laird's second-half goal gave Millwall victory in a bad-tempered game and took them to third in the table.
Tranmere had the better chances on an afternoon of petty fouls, with Millwall keeper David Forde saving Ben Chorley's volley and twice tipping over the bar.
Millwall's on-loan striker Izale McLeod fired against the bar, but Laird timed his run superbly to head the winner from David Martin's left-wing cross.
Chris Shuker twice went close and Forde tipped over Edrissa Sonko's header.
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