His side had been uncertain of progress following defeat in the first leg but eased ahead in Fife.
Geggan had spent the night in hospital following the first leg as a result of a kidney problem but the midfielder returned to lead his team in their hour of need. He led by example, too, scoring two of their goals to set up a play-off final with their Fife rivals.
"In the first leg one of their players hit my kidney and I went to hospital with chest pains," said Geggan. "I thought I would miss the second leg but I felt alright and I wanted to play through any pain barrier to get us through.
"Stranraer defended strongly but we knew one goal would take it to extra time and the boys were tremendous. We missed a lot of chances in the first half but when we levelled the tie it gave us the impetus to go on.
"We face two of the biggest games of our lives against Cowdenbeath as getting to the Championship with Rangers and Hearts there is massive. I do not know a lot about Cowdenbeath other than Kane Hemmings is very good but we are confident we can win promotion."
Dunfermline laid siege to the visitors' goal from the start and Geggan came close to opening the scoring when he struck the crossbar with a shot. He was not denied on the hour mark, though, and scored from close range after Faissal El Bakhtaoui's initial shot deflected off Scott Rumsby.
That goal took the tie into extra time and Geggan scored again with a thumping header following Danny Grainger's free-kick. The Fife side made sure of victory when El Bakhtaoui turned in a third goal.