Goals from Nick Locke and Kieran Mitchell in the second half helped the away side come from behind to shock Shire, and dump them out of the cup at home after going into the match as slight favourites.
Speaking to the Herald, the midfielder said: “We knew it was going to be a difficult game and sure enough it transpired to be just that on the day.
"They are are a very good side and they spent a fair bit on money in the summer, so in a semi-final against a local rival, it was never going to be easy.
"We were almost lucky to go in at the break just a goal down because they were on top and the line didn’t feel quite right at the back.
"They had a number of chances and so did we but they deserved to be in front at that point.”
After a poor showing before the the break, Bo’ness came out after the interval looking like a different side.
On the second-half showing he added: “We rolled our sleeves up for that second-half and we were the better team.
"I don’t think anyone could argue that we didn’t deserve to go through.
"They have great movement and we just had to work better within our shape, and we did that.
"Our organisation was much better and we made them resort to long balls and we got tighter.”
Having finished a mainly below-par Scottish Lowland Football League campaign in 10th spot, Bo’ness have finished with a flurry winning five away matches on the bounce.
Gemmell admitted overall he wasn’t best pleased with how the season has gone.
"It’s not been the best of campaigns, but that is down to us and what we have put out onto the pitch,” he said.
"We have so many good players in there and that is why it is frustrating talking about the season as a whole.
"Our max-capacity wasn’t reached and we could have done better individually but we showed it today.
"The second goal was a real bit of class, of course Nick Locke’s was a beauty but the way we constructed the first from Kieran Mitchell was a wee bit special.”
Opponents in the final EK beat Bo’ness 6-0 just last month in the league, and he admits it will be a tough outing.
Gemmell said: “They are a top side with a load of good players so we will go into the match knowing it will be a tough, tough game.
“We will need two second-half performances if we want to win the cup next weekend, but we will give it our best shot.”