Mowatt struck a spectacular free-kick the day after his 20th birthday to move his side eight points away from the relegation zone and leave the Lions still in the bottom three.
Luke Murphy was again in outstanding form in the Leeds engine room as they made it four victories in five league games.
Millwall had won only once at Leeds since 1988, losing on their last three visits, but victories at Nottingham Forest and Birmingham had offered manager Ian Holloway fresh hope.
Holloway included Angel Martinez in place of Michael Tonge, who joined on loan from Leeds last month but was prevented from playing by the terms of the deal.
Sam Byram, a scorer in Leeds’ 2-0 win at Reading in midweek, shot fractionally wide of the far post after a delightful passing move involving Mowatt and Charlie Taylor as early as the eighth minute.
But Millwall also stitched some impressive passes together, with Diego Fabbrini and Castleford-born winger Martyn Woolford to the fore.
Referee Paul Tierney had strong words with Millwall’s tall striker Stefan Maierhofer, who appeared to hit the deck too easily in a spat with Leeds defender Giuseppe Bellusci.
Maierhofer showed admirable control to bring down Dan Harding’s long ball moments later but his shot from distance was comfortably saved by Marco Silvestri.
There was danger for Millwall when Shaun Williams impeded Byram inches to the left of the penalty box, only for Luke Murphy’s twice-taken free-kick to be headed wide by home captain Sol Bamba.
However, Leeds opened the scoring in the 39th minute when Shaun Williams was penalised just outside the penalty area and Mowatt’s left-footed free-kick rocketed inside David Forde’s left post, taking a slight deflection on its way.
Forde saved a rasping volley from Rodolph Austin before racing off his line to close down Steve Morison, who spent the whole of last season on loan at The Den.
Millwall began the second half with Lee Gregory in place of Maierhofer, but Leeds maintained their high tempo and Morison headed over the bar when he should have tested Forde.
Holloway made a double substitution on the hour, replacing Martinez and Fabbrini with Edward Upson and Ricardo Fuller, but Woolford fluffed the Lions’ best chance by firing over after Bellusci had lost possession to Gregory.
Leeds fans were willing Morison to score his first goal since returning to the club in the summer but he wasted another chance by shooting well wide of the far upright, while Woolford almost grabbed an equaliser as his 25-yard drive zipped outside the foot of a post.