In the 38th minute of a dull first half Buddies striker Steven Thompson headed the visitors into the lead from a Gary Teale corner and it looked like the woes of the rock-bottom Fifers would continue.
However, a half-time team talk from Jefferies worked wonders as Joe Cardle levelled within a minute of the restart and, although the home side could not go on to find a winner, they moved to within three points of second-bottom Hibernian, who lost at home to Dundee United.
Dunfermline are still looking for their first home win of the season, but Jefferies, who was given a good reception by the home fans as he made his way along the touchline to the dugout before the game, will have seen enough him to encourage him.
The former Hearts boss made one change with midfielder Mark Kerr coming in for Ryan Thomson who dropped out of the squad altogether.
Dougie Imrie and Paul McGowan returned to the St Mirren midfield with Hugh Murray and Steven Thomson both starting on the bench.
On the face of it, though, the Fifers had little to fear.
Jefferies, though, would have seen in the first half why his new charges were struggling at the bottom of the table.
In the third minute Pars striker Liam Buchanan had a weak strike from inside the box easily saved by Saints keeper Craig Samson before Andy Dowie headed a Cardle corner over the bar, but the early stages were largely uninspiring.
The home side were the more positive, but rather than patiently build they mostly attempted to find a way through via the power of Martin Hardie, who was having his share of success in his aerial duels.
The ball was too often in the air, however, for either side to gain the ascendancy, while Saints skipper Jim Goodwin, booked in the 12th minute for a foul on David Graham, skated on thin ice with some more robust challenges.
The Buddies were going nowhere fast, although in the 27th minute defender Lee Mair volleyed high over the bar from 12 yards when he ought to have hit the target.
Therefore, it came as something of a surprise, although perhaps not to the suffering home supporters, when St Mirren found themselves a goal to the good.
Teale fired in a corner from the left and Thompson had space aplenty to redirect the ball towards goal and it cannoned in off helpless Pars midfielder Gary Mason who had been guarding the back post.
Jefferies' team talk at the break did the trick.
After Hardie flicked on Mason's pass inside the box, Mair and Buchanan tussled for possession and, as the home fans screamed for a penalty, referee Alan Muir allowed play to continue long enough for Cardle to scramble the loose ball in from close range.
Moments later, as the rejuvenated Fifers pressed again, Carey cleared Mason's low drive off line before Samson had to make a save at his near post from Cardle.
Play swung from end to end as St Mirren shook themselves down and rolled their sleeves up again.
As the Buddies reasserted themselves Hasselbaink headed a Carey cross high over the bar.
In the 78th minute Thompson headed a Goodwin free-kick wide of the target before Dowie bravely put his head in front of a goalbound drive by McGowan.
Dunfermline fans roared their team forward in the final minutes, but it was McGowan who flashed an angled shot wide in injury time before Pars defender Alex Keddie had a shot blocked at the other end.