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The 30-year-old bagged his eighth goal of the season 15 minutes from time to follow on from Sunderland loan-man Jonathan Stead's opener three minutes earlier as the high-flying Rams made it four wins in a row.
The unrest surrounding Kenilworth Road was added to by fans distributing 4,000 leaflets around the ground demanding the resignation of chairman Bill Tomlins.
Luton started well and threatened a minute in when Ahmet Brkovic and Adam Boyd combined to release Rowan Vine down the left, but the former Portsmouth man could only blast his angled left-footed shot across the face of goal and out for a throw-in.
The hosts knew they would have to keep a close eye on in-form Howard, but they couldn't stop their ex-player teeing up Stead for a fifth minute left-footed strike that whistled just past the post.
After Morten Bisgaard's tumble in the area under Lewis Emanuel's challenge was ignored by referee Steve Tanner, Stead tried his luck again in the 17th minute when he fired a right-footed effort a yard over the bar from the edge of the area after Seth Johnson's cut-back.
Luton finally got their act together and fashioned an opening in the 21st minute when Markus Heikkinen nodded back Steve Robinson's header into the area for Russell Perrett to hit a 12-yard left-foot volley that Stephen Bywater saved.
Derby continued to look dangerous though and Matt Oakley's burst to the right-hand by-line in the 26th minute saw him produce a dangerous low cross that Perrett almost diverted past his own goalkeeper only for Marlon Beresford to gather.
Emanuel then blasted a cross-shot past the post from wide out on the left after Marc Edworthy had half-cleared a Vine cross before Derby squandered the clearest chance of the half in the 32nd minute.
Oakley was again the provider with another burst from left to right which allowed him to cross for Bisgaard, who could only volley wastefully over the bar from eight yards.
Luton finished the half with a flourish as Bywater had to stretch to tip over Leon Barnett's looping 16-yard header from Kevin Foley's 36th minute cross.
Luton were almost caught cold after the interval when Marc Edworthy fed Stead to turn and shoot from the edge of the area only to see his low strike bounce back off the foot of the post.
Busy Adam Boyd responded for Luton with a 22-yard left-foot strike wide of the target after a one-two with Edwards in the 50th minute before Derby's Giles Barnes ended a driving 30-yard run with a fierce 20-yard shot that flew inches past the post.
The game spluttered through a scrappy period of play before Derby took the lead with a stunning strike from Stead in the 72nd minute.
After Luton had only half-cleared a corner, the ball found its way to the striker on the left-hand corner of the penalty area. He side-stepped Perrett before unleashing a powerful right-footed strike that gave Beresford no chance.
Three minutes later the game was effectively over when Howard grabbed the Rams' second.
A clever free-kick routine saw Johnson tee up Oakley to cross from the right. Bisgaard saw his close-range effort come back off the post and Howard was first to react to slam home from two yards.
Luton rallied late on as substitute Warren Feeney saw a header cleared off the line by Oakley and Boyd hit a 20-yarder just wide, but it was too little too late.