But in a thrilling start to the game for both sets of supporters, Luke Pyman headed home for Leighton and it was 1-1 with less than ten minutes on the clock.
The Bell Close side then went ahead, 2-1, thanks to Duncan Culley’s strike 20 minutes into the action-packed final.
Just before half time, the game changed with a controversial red card for Bedford’s Charley Sanders for a tackle on Culley.
In the second-half, with chances for both sides, ten-man Bedford kept the score at 2-1 until stoppage time. When it looked all over, Rory McAuley earned Eagles the latest of lifelines with his 97th-minute equaliser, taking the tie to a penalty shoot-out.
While it was ecstasy for Gary Setchell and the Bedford contingent, it was agony for the Leighton fans who had been just seconds away from celebrating victory.
But after the heartache of conceding the late goal, the Leighton players kept their heads to win 5-3 on spot kicks.
It was Leighton’s second giant-killing win on penalties in the cup, having knocked out a young Luton Town side in the quarter-finals.
Leighton lifted their first silverware under manager Lee Bircham, who only took over the side last month with just six games of the season to go. They have finished their league campaign fourth in the Spartan South Midlands Premier Division.
Bedford, having secured promotion to Step 3 after a truly outstanding season, will be disappointed to miss out on the league and cup double but still have their Southern League Championship game on Saturday, when they host Division One South champions Plymouth Parkway at the Eyrie.