After going a goal down in the first-half from Joao Victoria, Max Christie’s side rallied and replied through Gregor Nicol early on after the break.
But EK proved too strong on the day for a depleted and drained Bo’ness as their Lowland League rivals sealed the cup, with goals from Liam Watt, Cameron Elliot and Neil McLaughlin.
Bo’ness had the first chance of the final moments after kick-off, with Lennon Walker firing over from outside the area in what was a positive start from the underdogs.
They started on the front foot and with seven minutes on the clock, semi-final match winner Nick Locke forced Connor Brennan into a smart stop from a free-kick.
Striker Kieran Mitchell was next to test the EK goalkeeper when captain Michael Gemmell sent him through on goal over the top.
One-on-one his shot was well parried by the Lowland League ‘keeper of the year, who is joining Stenhousemuir this summer.
Gemmell was next to go for goal on the half hour mark missing by a fair margin on the turn from 25-yards.
EK hadn’t threatened Christie’s side too much, with Victoria up top causing the Bo’ness defence problems with his running ability, but Andy Murphy was yet to face a shot at goal.
Victoria floated in a cross to the back post that McLaughlin blasted over from close range, much to the relief of the Bo’ness backline.
On 39 minutes, EK opened the scoring through Victoria, the striker was played in behind and he finished calmly past Murphy to put them in the lead.
Murphy kept them in the match just before the break when he diverted Elliot’s effort onto the bar when it looked destined for the top corner.
Bo’ness weathered a storm in the early part of the second-half, with Kevin Rutkiewicz’s side looking to double their advantage.
McLaughlin sent a dangerous volley arrowing wide with Gemmell making a number of key interceptions to deny EK advances forward.
But a dogged Bo’ness outfit stayed in the tie and they grabbed an equaliser from a corner on 55 minutes.
Winger Gregor Nicol looped a header home after a deep delivery from Keir Mcauley caused havoc in the EK box to level the cup final.
Moments after kick-off, Murphy made a brilliant save to deny Elliot who found a way through a packed defence to have a shot at goal on the angle.
On 63 minutes, EK retook the lead through a wonderful strike from Liam Watt, who curled an effort out of Murphy’s reach after some slack Bo’ness demanding was punished on the wing by Victoria.
They should have put the tie beyond Bo’ness but Murphy was a man on a mission and saved well again when substitute Daniel McManus shot from close range.
With 20 minutes to go, Elliot darted in behind from a free-kick and slotted home past Murphy to put the tie beyond Bo’ness.
Bo’ness brought on defender and assistant manager Stuart Hunter as their last role of the dice to get back into the game.
But the opponents on the day were just too strong in the second-half and on 80 minutes McLaughlin made it 4-1 with a stunning effort just on the edge of the area.
Walker did grab one back in the final moments for Bo’ness, finishing well in the area under pressure, but it was too little too late.
1. Andy Murphy
3. Ryan Stevenson
4. Greg Skinner
6. Michael Gemmell (c)
7. Gregor Nicol
9. Kieran Mitchell
10. Nick Locke
12. Devon Jacobs
16. Keir Macauley
18. Kyle Johnston
19. Lennon Walker
5. Stuart Hunter
15. Lewis Hawkins