The league leaders were on course for a setback in their promotion bid but Howard scored with a typical towering header.
It took the glory away from Oldham striker Luke Beckett who marked his debut with a goal after joining on loan from Sheffield United until the end of the season.
Struggling Oldham have also brought in defender Gareth Owen on loan from Stoke City but both men were left disappointed by Howard's late intervention.
Luton went ahead on six minutes when Paul Underwood seized on a loose ball 12 yards out and sent a superb dipping volley up and over Oldham keeper Steve Mildenhall.
Oldham fought back as Beckett linked with strike partner Chris Killen before forcing Luton keeper Marlon Beresford to pull off a fine save.
Beckett also had a header cleared off the line and took a crucial role in the Oldham equaliser six minutes before half time.
His pass sent Killen through and the New Zealand international drove his shot into the bottom corner from the edge of the box.
Killen went close to another just after half time but it was Beckett who put the Latics in front when he cut out a weak back pass from Chris Coyne and rounded the keeper to score from a tight angle.
Sol Davis shot at Mildenhall after a strong run but Luton appeared beaten as the game went into its last minute.
Howard had other ideas though and jumped to meet a right-wing cross from Peter Holmes to send his header into the top corner from eight yards.