Swiss goalkeeper Jakupovic, who has played second fiddle to David Marshall in the Premier League this season, saved penalties from Jonjo Shelvey and Yoan Gouffran, while Newcastle striker Dwight Gayle’s spot-kick hit the crossbar.
Hull, who levelled through Robert Snodgrass within a minute of Mo Diame’s opener for Newcastle in the first period of extra time, were clinical with their penalties as Snodgrass, captain Michael Dawson and Tom Huddlestone were all on target.
“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.”
Phelan, a League Cup winner with Manchester United in 1992, admitted his side had not practiced penalties before the quarter-final.
“I’ve never even thought about penalties to be fair,” he said. “If I’d have had it my way I wouldn’t have wanted to go that far because we have a very important (Premier League) game on Monday (against Middlesbrough).
“I thought our penalties were very clinical and under that spotlight they all executed them very well.”
The Tigers played the whole of extra time with 10 men after striker Dieumerci Mbokani had been shown a straight red card in the 89th minute for reacting furiously to Jamaal Lascelles’ tackle from behind.
Phelan said he was disappointed with Mbokani for retaliating, but also sympathised with the DR Congo international because he felt referee Neil Swarbrick offered him no protection throughout the match.
But the former assistant to Sir Alex Ferguson preferred to focus on his side’s resilience after another dogged display edged them to within touching distance of Wembley.
“For this football club it’s a tremendous achievement because this is the furthest they’ve ever been.
“The players are really pleased with that. It gives them something in Rothman’s (Football Yearbook) now or what have you, where they can say they’ve got to a semi-final of the competition.
“Hopefully they can go one step further. They worked hard enough tonight to get their reward.”
Newcastle boss Rafael Benitez felt his side had been punished for failing to take their chances in normal time when they had clearly held the upper hand.
“You have to be disappointed,” the Spaniard said. “The way we played we deserved to score goals in the first half and in extra time.”