The Bluebirds led through Sol Bamba’s header before Ngbakoto equalised five minutes after coming on as a second-half substitute.
And Ngbakoto’s corner with seven minutes remaining was met by Matt Smith, with the ball going in off Cardiff defender Jazz Richards.
Ngbakoto, whose father died shortly after his summer move from Metz, initially struggled for fitness and form but has looked much sharper in recent weeks.
Holloway said: “He’s been very patient. I’ve asked him to do some fitness work behind the scenes and he’s lost all sorts of poundage.
“He had a terrible bereavement just after he joined us and I felt that affected him, but he’s one of our family and he’s an absolute joy to work with.
“He’s made another statement there for me to pick him.”
The result meant a losing return for Cardiff’s former QPR manager Neil Warnock on the day Rangers marked the 50th anniversary of their 1967 League Cup triumph.
Holloway’s players wore a special edition all-white kit in honour of the one worn by the Wembley-winning team managed by the late Alec Stock, and several members of that side were presented to the crowd at half-time.
Holloway said: “Today, honouring the people who are famous to all us QPR people, to have them here and to come out and win, I’m delighted.
“We came from behind and sometimes you need your substitutes to do it.
“Yeni’s first goal was a great move and that gave us the impetus to go and get another one.
“It was a competitive game, but what else do you expect with two competitive people in the dugout who love QPR – and Neil now loves Cardiff.
“Neil will be fuming, but there wasn’t a lot between us and I did feel our substitutes coming off the bench made the difference for us, and I’m delighted for them.”
Warnock felt Cardiff’s defeat underlined why he believes they will miss out on a play-off place, despite an excellent recent run.
“I’ve been saying for months we’re not going to do it,” Warnock said.
“If we can’t win here when we dominate like that we’re not going to make the play-offs.
“We were 1-0 up and really should have scored two or three goals in the second half. To then give them a chance is very disappointing.
“But to get where we are has been fabulous. The lads have really done well for me.
“We’re looking to next season. I’m learning all the time – I saw one or two things today which is really helping me to decide what I’m going to do at the end of the season.
“I was pleased to see those things. It answered a few questions for me, although I was disappointed to lose.
“I’m looking all the time to see what we need to have a good go next year. I thought today just helped make my mind up on a few positions.”