Following a disappointing lack of goalmouth action and entertainment, the tie came to life during the dying stages. The captain Andy Geggan gave the visitors a 77th-minute lead from Danny Grainger's long throw, but Thomas O'Brien levelled six minutes later when he headed in another throw, from Rory McKeown.
More than 2500 Dunfermline supporters made the short trip along the A92 for the latest instalment of Fife's oldest derby and they had good reason to be confident, with their side having won 10 out of the last 11 meetings - including last July's League Cup tie.
The visiting players showed their support to team-mate Jordan Moore, who is fighting skin cancer, during the warm-up by wearing T-shirts with the on-loan Dundee United striker's name emblazoned across both sides.
Chances were at a premium during a tense start and Cowdenbeath defender Darren Brownlie headed over a McKeown corner when he should have found the target.
After 34 minutes, a deep Ryan Williamson cross found Ryan Thomson but the forward, under pressure from the home goalkeeper Thomas Flynn, headed wide from close range.
Josh Falkingham was then bailed out by Dunfermline team-mate Grainger after his attempted pass-back was cut out by Greg Stewart. The left-back read the danger and forced the forward into a foul.
At the other end, the Dunfermline striker Faissal El Bakhtaoui was found in the box by Andy Geggan moments later but the French-Moroccan lashed wide from a tight angle.
Cowdenbeath should have gone in at the break ahead after Kane Hemmings raced clear of Alex Whittle following Armstrong's clearance of a corner, but Scully spread himself to repel the Scotland PFA Championship Player of the Year's effort.
Kerr Young became the fourth player to be booked in the game when he tripped Hemmings seconds after the restart, but McKeown could only find the side-netting with the free-kick.
With Dunfermline needing extra-time on Saturday to see off Stranraer, it was no surprise to see manager Jim Jefferies turn to the bench in the second half to add fresh legs to his side, with Allan Smith and Ross Forbes both coming on.
That breakthrough finally came in the 77th minute and it was no surprise it was from a deal-ball situation. Grainger's long throw made its way to the back post and Geggan rose high to force a header home and send the away support into raptures.
But that lead lasted just six minutes and from another McKeown long-throw, O'Brien was afforded space to head in from close range to deny Dunfermline a head start in the return at East End Park.