Jacob Brown's early strike set up Stoke City's first win in nine games as they dealt a blow to Millwall's Championship play-off hopes.
Brown nodded in Lewis Baker's corner to put the Potters in control before George Saville's own goal made it 2-0.
Stoke dominated and should have scored more - although Jed Wallace might have reduced the deficit after Tom Bradshaw was fouled in the box.
However, Jack Bonham saved Wallace's penalty and the home side went on to close out the game.
Defeat brought the Lions' eight-match unbeaten run to an end, leaving them four points outside the top six, and eased the pressure on Stoke manager Michael O'Neill.