Popa (pictured), who had joined the game as a 70th minute substitute, was bundled over in the Leeds box in the final minute and duly scored with the subsequent spot-kick after sending Leeds 'keeper Ross Turnbull the wrong way.
Development Squad Coach Richard Beale was delighted to see his side - who came through a tough Birmingham Senior Cup tie on penalties only three days earlier - victorious in what he described as 'an entertaining game'.
"From the first minute we played with a really good intensity," he said.
"Everybody was at it and the pressure that we applied off the ball was at the level we want and require.
"Young players often just stand off people, but we've had a chat about it over the last couple of weeks and we were really good in pressuring them.
"We played on the front foot and really got about them in a strong and tough manner which you've got to do when you come away to places like Leeds.
"We didn't let them settle on the ball and we didn't let them play their game and we broke on them and had numerous counter-attacks and we looked a threat on the break.
"There weren't loads of chances, but it was an entertaining game nonetheless and both teams were obviously going for the win."
Blues Under-23s: Trueman, Kwiecien, Martin, Maxwell, Seddon, McCoy, Popa 70), O'Keeffe, Baba, McDonald (Mulders, 90+1), Lubala (Kebbie, 90), Storer.