The Republic of Ireland striker only started due to an injury to Lions top scorer Darius Henderson, but he made his mark by grabbing the winner with 14 minutes to go.
Derby rookie Will Hughes, who earned a call-up to the England Under-21 squad this week, had earlier cancelled out a controversial opener from Liam Feeney.
Millwall were not only without Henderson and in-form winger James Henry through injury, but manager Kenny Jackett was also absent, laid low through illness.
Rams keeper Adam Legzdins dealt with a couple of early long-range efforts from Liam Trotter and Chris Wood before Shane Lowry's shot from a half-cleared corner was blocked by Hughes.
But it was Feeney, himself only recalled to the side due to Henry's injury, who broke the deadlock in the 33rd minute with a first-time shot from Chris Taylor's cross.
His celebrations were initially curtailed by an offside flag but referee Graham Salisbury consulted with his assistant before signalling for a goal.
The Lions could have doubled their lead before the interval when Keogh curled the ball into the area but Wood was inches away from getting the crucial touch.
Derby only created a couple of half chances in the first period with Hughes seeing a shot blocked by Danny Shittu and Richard Keogh firing over from long range.
Millwall continued where they left off at the start of the second half with Feeney firing narrowly wide and Lowry heading over from a corner.
However, the Rams grabbed a shock equaliser in the 53rd minute when Craig Bryson laid the ball off for Hughes and the 17-year-old crashed in his second senior goal from 20 yards.
But Millwall regained the lead and stretched their unbeaten run to nine matches when Scott Malone laid Feeney's long ball off to Keogh, who neatly tucked in his fifth goal of the season.
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