Kirk headed in a 68th-minute cross from Joe Cardle, who had put the Pars in front 12 minutes earlier, before capitalising on a defensive mix-up for a third after 77 minutes as the Pars celebrated a first home win of the campaign.
The result saw Jim Jefferies' men end a 12-match winless run but more importantly cut the gap to Hibs, who play St Mirren tomorrow, while the eighth-placed Dons, who lacked a cutting edge throughout, are now four points adrift of Kilmarnock.
It was Jefferies' first win as Pars boss since succeeding Jim McIntyre last month and the former Hearts manager has avoided defeat in three of his five matches in charge.
Dunfermline had not won since January 21 at Kilmarnock and after 18 attempts now have succeeded in delivering a home win.
Attention now turns to Paisley tomorrow before Hibs tackle Aberdeen on Wednesday, when the Pars travel to Inverness.
The May 7 meeting between William Hill Scottish Cup finalists Hibs and Dunfermline at Easter Road could yet prove decisive in the battle to avoid the drop.
Kirk's late strike last week at St Mirren saw Dunfermline claim a 4-4 draw and narrow the deficit at the foot of the standings and the striker was one of three changes for the Pars, with Paddy Boyle and Cardle also starting in place of Austin McCann, Jordan McMillan and Liam Buchanan.
The Dons, who made two changes from the side which won 2-0 at Inverness, with Scott Vernon and Chris Clark coming in, have begun preparations for next term and six players were this week told they are surplus to requirements.
Goalkeeper Jamie Langfield, along with Josh Magennis, was offered a new contract, but in his second SPL fixture of the season gifted the Pars an early opportunity.
Langfield picked up Gavin Rae's back-pass and was booked for his protests before Martin Hardie fired wide across goal from the resulting indirect free-kick.
Vernon was proving a nuisance up front but the Dons were unable to capitalise, the final ball repeatedly letting them down and Fraser Fyvie and Mitchel Megginson fluffing attempts on goal.
A Rae effort deflected out for the first of a series of three corners in quick succession which the Pars scrambled clear as Aberdeen continued to push forward without really threatening.
Magennis bundled over Cardle but Hardie's set-piece hit the wall before Vernon failed to connect with a Clark cross at the other end as the first half ended goalless.
The Pars were second best at the start of the second period but took the lead after Alex Keddie's long ball upfield caused a defensive mix-up between Magennis and Ryan Jack as Aberdeen's afternoon became even more lacklustre.
Winger Cardle took advantage, cutting in from the left on to his right foot and tucking in his eighth of the season.
The Dons made a change, with striker Darren Mackie, who this week was informed his 13-year career at Pittodrie will finish at the end of the season, replacing Megginson, but were soon two down.
Cardle's inswinging free-kick found an unmarked Kirk on the edge of the six-yard box to head beyond Langfield.
Further defensive calamity from Aberdeen gifted the hosts a third.
Langfield found Fyvie, whose attempt to return the ball to the goalkeeper was intercepted by Kirk.
The Dons stopper got a hand to his shot but it was too powerful as the Pars triumphed to pile the pressure on Hibs.
