The Tigers secured a spot in the semi-finals via a penalty shoot-out and Jakupovic saved efforts from Jonjo Shelvey and Yoan Gouffran.
Phelan was delighted with the keeper's display and hailed the "focus" of his players, as Robert Snodgrass, Michael Dawson and Tom Huddlestone scored their spot-kicks to send Hull into the last four.
"I'm pleased for Eldin, I'm pleased for all of them," said Phelan. "Eldin's been in the cup competitions all the way through.
"He's performed well tonight and going into the penalty shoot-out he was probably the right goalkeeper to have there because his record is pretty good in those situations.
"I brought in another good goalkeeper and we've now got two good goalkeepers. Allan McGregor's on his recovery, so we may end up with three terrific goalkeepers and we may have to use them.
"It's important they stay focused. Eldin's done that. He's taken his opportunity tonight, he's probably been the hero and hopefully he'll be a hero again."