Nigeria defender Taye Taiwo converted the spot-kick, awarded after defender Yoann Lachor unwittingly handled the ball in the area, to put Marseille on 68 points from 33 games.
Midfielder Mathieu Valbuena put Marseille ahead with an angled shot from inside the box shortly before halftime but Boulogne fought bravely and equalised courtesy of a late goal from close range by substitute forward Jeremy Blayac.
"We would have been happy with just one point because, frankly, what we showed tonight was not good," Marseille sports director Jose Anigo told his club's website.
"We have our little cushion (of points) but we're not going to celebrate because 15 points are still to play for," he added.
Marseille faced a 1,000-kilometre coach ride home because of the closure of most airports in the country with a cloud of volcanic ash hanging over northern and central Europe.
They did not really mind, however, after moving closer to their first league title since 1992.
"Fourteen hours by bus to go back to Marseille will give the players an idea of what our fans go through when they come to away matches," Anigo said.
With five games to play, the former European champions remained five points ahead of surprise package Auxerre, who crushed mid-table Lorient 4-1.
Champions Girondins Bordeaux and Olympique Lyon did their slim title hopes no favours when they drew 2-2 in a tense game in Bordeaux featuring three red cards in the last minute.
Lyon defender Anthony Reveillere was the first to receive his marching orders, for a nasty tackle on Benoit Tremoulinas, who was sent off together with Bordeaux team mate Jussie in the heated argument that followed.
Bordeaux led twice, with goals from Morocco striker Marouane Chamakh and Czech midfielder Jaroslav Plasil, but Lyon, who knocked out Bordeaux in the quarter-finals of the Champions League, levelled each time, through Brazilian midfielder Ederson and Brazilian defender Cris.
Lyon and Bordeaux stick to third and fifth place and are now nine and 11 points off the pace respectively.
