Luton had welcomed home-town England cricketing hero Monty Panesar on to the pitch before the game.
But it was Howard who had the Tractorboys in a spin as he headed home nine minutes from time to settle a scrappy affair.
Howard almost made it two as he was denied by impressive visiting teenage goalkeeper Shane Supple at the death and substitute Warren Feeney smashed over from six yards in injury time as Luton grabbed a deserved win.
In a quiet opening period the only chance of note came in the ninth minute when Carlos Edwards' pull back from the right found Dean Morgan, but the former Reading man could only slice his shot well wide from the edge of the penalty area.
The first meaningful chance came 60 seconds later for Ipswich when Richard Naylor controlled a long Supple clearance and laid off to Darren Currie, who saw his 24-yard effort pushed over by Marlon Bereford.
Luton lifted themselves after the break and twice went close in the space of a minute.
Firstly Chris Coyne hit a raking 51st minute free-kick over the head of visiting full-back Castro Sito allowing Morgan to chest the ball down but drive over the bar from 14 yards.
Moments later Ipswich left-back Jay McEveley saw his back header fall short and Rowan Vine latched on to the ball only to fire into the side-netting with just Supple to beat.
Supple then had to be alert in the 54th minute when Vine beat Sito with a mazy run and crossed for Edwards to strike a low 12-yard volley that the teenage goalkeeper did superbly well to turn around the post.
The visitors rallied with a 20-yard Jimmy Juan shot that rolled wide in the 58th minute before Alan Lee fired weakly at Beresford from the edge of the area after smart interplay between Naylor and Currie.
But with the game looking to be heading towards a stalemate, the Hatters sealed the points nine minutes from time when substitute Ahmet Brkovic crossed from the left for Howard to glance home his fourth goal in the last six games from 12 yards.