Blues struck first in the Premier League Cup fixture, which was played at Nuneaton Town’s Liberty Way Stadium, after David Popa swept the ball home on the half-hour mark.
But the Potters levelled proceedings just before the break through Hakim Abdallah.
However, Blues found themselves back in front minutes after the restart when O’Keeffe fired home from 30 yards into the top corner.
Blues Development Squad Coach Richard Beale felt his youthful side thoroughly deserved their victory.
“It was a very good performance and the levels from all the players was exceptional," he said.
“We had a really young team out and I was delighted with the way the boys stepped up to the plate.
“They showed fantastic commitment and energy throughout the game.
“We stuck to the game plan and beat a Premier League club, which was warranted.
“We did the basics really well, we competed, fought, tackled and earned the right to play first and foremost, and when we did play we put together some really good moves.
"It was the type of performance I’d like to see from the lads every week.”
Beale reserved special praise for O’Keeffe (pictured), who capped off an excellent performance with a fine goal.
“Corey O’Keefe was unbelievable on the day,” added Beale.
“He had a fantastic game and it was nice for his performance to be capped with the winning goal.”
Blues Under-23s: Trueman; O’Keeffe, Mulders, Martin, Cleary, (Yuill, 24), McCoy, Baba, Maxwell, Storer (Matteo Polisi, 70), Popa, McDonald.
Subs not used: Weaver.