Doug Sheppard’s men went into the second leg of the final with a 4-1 advantage and looked set to run out comfortable winners after the opening period, Aaron Connolly and Tomas Karpov strikes stretching the aggregate lead to five goals.
However, Milton Keynes hit back, levelling the match at 2-2 before the end of the second period, while two further goals moved the visitors within one of the Bison on aggregate with just over seven minutes to play.
The home fans were on the edge of their seats for a while, but Andy Melachrino saved the day, finding the net with less than four minutes left to tie up a 7-5 aggregate victory, sending the majority of the 1,300-strong crowd wild.
It was difficult to see such a dramatic finale coming to pass in the opening 20 minutes.
The Bison made the perfect start, Connolly finding the net from the left wing after just 40 seconds to extend the lead to 5-1 on aggregate.
The hosts continued to pile on the pressure, with Nicky Chinn going close and Milton Keynes goalkeeper Stephen Wall keeping his side in the game.
Dean Skinns did not make his first save of note until midway through the period, denying Leigh Jamieson, but the Bison then went down the other end and doubled their advantage on the night.
With the Lightning’s Jordan Cownie in the sin-bin, Basingstoke’s top marksman, Karpov, tipped home Miroslav Vantroba’s blue-line shot.
Ciaran Long became the first Bison player to take a penalty as the visitors got on top towards the end of the period, but Skinns was on top form to deny first Stanislav Lascek and then Grant McPherson.
Milton Keynes made them pay on the third powerplay at 27:02, Jamieson tapping in the rebound after Ross Green’s shot was saved.
The Bison hit back, with Karpov going close on the powerplay and Melachrino forcing Wall into another save, but the visitors saw out the storm and were able to regain the upper hand.
Skinns made two more top saves, denying Adam Carr and Michael Farn, but could not prevent Carr levelling the match from close range at 37:58.
Basingstoke remained three goals clear at 6-3 but the momentum was with the visitors. They took the lead on the night at 43:56, Stanislav Lascek firing over Skinns from a Blaz Emersic assist, with Baird again in the sin-bin.
The Lightning were rampant and went close to reducing the aggregate lead to a single goal when Lukas Zatopek fired a shot into the chest of Skinns.
Joe Rand went close during a rare Bison attack, with Lascek forcing a save from Skinns at the other end, while the Bison suffered a major setback going into the final 10 minutes.
Import defenceman Vantroba was sent to the sin-bin for tripping but then spoke out of turn to the officials, earning himself a 10-minute misconduct penalty.
Things got even worse at 52:12, when Jamieson’s long-range strike reduced the Bison’s lead to a single goal at 6-5.
Fingernails were being bitten to the quick around the arena as Milton Keynes pressed for an equaliser, but they were handed a reprieve when McPherson departed for high sticks at 56:08.
The hosts needed just 16 seconds of the resulting powerplay to give themselves some breathing space, Melachrino touching home a Kurt Reynolds shot from the blue line to release the tension somewhat.
The Herd played out the final three minutes without further incident to secure the EPL Cup, sparking wild scenes of celebration both on and off the ice.
Bison players celebrate with the EPL Cup
Post-match reaction with Bison player/coach Doug Sheppard