Howell struck just before the hour as Wayne Scott’s side fought back after a poor first half and drew for the first time this campaign to remain just above the relegation positions.
Scott made seven changes from the side beaten at Newcastle. He gave a debut to new signing Kieron Walker and gave full debuts to Kieron Kenton-Bradshaw, Kofi Halliday and Tony Law. In addition, Wisdom Asare, Josh Rae and Romello Nangle all returned to the starting eleven, with goalkeeper Jack Steggles maintaining his place at the expense of the unavailable Curtis McDonald.
Carlton began brightly with some threatening crosses from Halliday in particular, but the Whites took the lead with their first attack on seven minutes. Kallum Smith was left all alone on the edge of the box from a Lincoln corner. His shot took a heavy deflection off Andrew Toyne to completely wrong-foot Steggles and nestle in the back of the net.
That was the springboard for a spell of Lincoln pressure that lasted for pretty much the whole of the first half.
Toyne had an excellent chance to double his tally on 14 minutes but fired wide from inside the area before a stunning Daniel Brooks free kick crashed against the post with Steggles beaten.
Tom McConway had managed to bring a decent save out of Sam Vince in the Whites goal but it was an all too rare advance by the visitors, who were struggling to maintain any possession at all.
Toyne saw another effort deflected wide before Brooks fired another free kick just wide of the post.
Scott replaced Asare with Daniel Gordon at half time and Carlton came out for the second half with a much more combative attitude.
Lincoln tried to score straight from the kick off as they shot from the centre-spot without passing the ball. Steggles sent the ball straight back up field and Rae fed the ball to Nangle who lifted the ball high over the bar when clean through on goal.
Lincoln played some fine football on the left hand side but were perhaps guilty of one pass too many as McConway made a goal-saving tackle in the penalty area.
The Millers then began a spell of pressure that led to the equaliser. McConway saw a corner cleared back to him. He fed Jake Wholey whose deep cross was only half cleared by Vince. Tony Law saw his shot deflected over the bar for another corner.
McConway took it again. Vince punched the ball to Gordon whose shot was cleared off the line by Toyne. Lincoln couldn’t get the ball away and it fell to Nangle who floated a deep cross to just beyond the back post where McConway was waiting.
He resisted the temptation to shoot at an almost impossible angle but instead flicked the ball delightfully to Howell who fired home on the half-volley from eight yards.
The Millers were inspired and Nangle fired just wide after a good run on the right.
As the game reached its closing stages Carlton seemed to back off and Lincoln pushed forward for a winner. Steggles made a superb save from Paul Grimes, holding onto his fiercely driven shot, before doing equally well with a cross from Matt Cotton.
At the other end substitute Kevin Lusamba brought a save from Vince before the referee brought the game to a conclusion.
Carlton Town: Steggles, Kenton-Bradshaw, Wholey, K Walker, Asare (Gordon 46), McConway, Nangle, Howell, T Law (Fletcher 86), Rae, Halliday (Lusamba 59). Unused subs: Maveso, J Law.
Goal: Howell 58.
Carlton Town Supporters Club MOTM: Jack Steggles