Dunfermline midfielder Joe Cardle pulled one back after 63 minutes to set up a nervous finish for the home side but Danny Lennon's men held out for the three points their play deserved.
The victory meant St Mirren moved up to fifth place in the Scottish Premier League.
The home started the match with an attacking mindset and Dunfermline goalkeeper Paul Gallagher was forced into good low stop from Jim Goodwin's long range strike after three minutes.
Two minutes later there were cries for a penalty when Paul McGowan's shot was blocked by Paul Burns just inside the penalty area but referee Crawford Allen waved play on.
St Mirren continued to threaten but Hasselbaink and Steven Thomson were both unable to find the target from promising positions.
Dunfermline looked to be struggling to contain their hosts and Gallagher again had to be at his best to turn McGowan's strike from distance round his post on 13 minutes.
From the resulting corner St Mirren defender Lee Mair found himself in space inside the area but his header from close range went wide of the post.
Lennon was forced to make a substitution after 18 minutes when he replaced the injured Steven Thomson with Graham Carey.
McGowan should have grabbed the game's opening goal after 22 minutes when Goodwin's excellent cross evaded the Dunfermline defence but the striker was unable to make any contact with the goal at his mercy.
The hosts finally got the goal their play merited after 25 minutes when Hasselbaink's weaving run ended with a neat cutback to Kenny McLean who slid the ball in from close range.
Dunfermline responded by creating their first chance of the match and Ryan Thomson passed up a glorious opportunity after an excellent delivery from Paul Willis - heading wide from eight yards out.
Hasselbaink was proving to be a constant threat to the Dunfermline defence and his superb delivery found Stephen Thompson who headed the ball across goal to McLean only for Gallagher to produce a wonderful stop from point-blank range.
St Mirren goalkeeper Craig Samson had been a virtual spectator during the first half but he was forced into an excellent save when Andy Kirk connected with Willis' dangerous free-kick.
On the stroke of half-time the home side doubled their lead.
Steven Thompson robbed Austin McCann inside the Dunfermline half and delivered a superb delivery which Hasselbaink converted in style.
St Mirren continued to enjoy the better of the play after the break and after 47 minutes Dunfermline defender Alex Keddie was forced to head the ball behind his own goal after good work by Hasselbaink.
Hasselbaink was involved again minutes later when he tested Gallagher from distance and he then turned provider for McLean who shot over from close range.
Dunfermline were struggling to offer any attacking threat and boss Jim McIntyre introduced Andy Barrowman and Joe Cardle in place of Paddy Boyle and Liam Buchanan in a bid to find his side a way back into the match.
It was the home side who continued to assert pressure though and Gallagher did well to parry away Graham Carey's free-kick.
On 62 minutes the St Mirren defence failed to deal with Cardle's cross and the ball deflected off Samson and into the goal.
St Mirren showed signs of anxiety after losing the goal and the visitors began to grow in stature.
Jim McIntyre made his final change of the match when he brought on Steven McDougall to replace Kirk.
Lennon responded by introducing Illias Haddad for Carey who had earlier come on as a substitute.
St Mirren began to regain a foothold on the match and Mark McAusland should have done better when he got on the end of McLean's dangerous corner.
Two minutes later Gallagher produced a brave low save at the feet of Steven Thompson after good work by David van Zanten.
Dunfermline substitute Cardle was causing the St Mirren defence problems and he unleashed a stinging effort after an excellent driving run, forcing Samson into a good stop.
A late effort from David Graham was as close as they were to come though and St Mirren held out for all three points.