Struggling Middlesbrough are now without a win in seven matches.
And boss Tony Mowbray admitted his lack of defensive options is a concern, especially as they await news on Jonathan Woodgate’s calf.
Without the suspended Rhys Williams, Mowbray gave 20-year-old Gibson a full league debut for the club and was forced to replace Woodgate at half-time.
Mowbray said: “I thought Gibson gave one of our best performances.
“For a young boy he’s got a voice and an understanding of defending.
“But the suspension of Williams left us short and Woodgate has not been 100 per cent.
“To go out and be a goal down after three or four minutes, especially against a team who haven’t been conceding goals, left us with a tough task.
“I’m sure that gave QPR a lot of belief and to give them such an early start was frustrating.
“There was a slight improvement in the second half but it wasn’t enough.
“That’s the fourth penalty in three games we’ve conceded.
“You’ve got to give yourself a chance to win football matches and to give the opposition chances like that is frustrating.
“We have to strive to be better and improve. We came here full of expectation that we could get something, but we didn’t and we didn’t deserve to.”
First-half goals from Joey Barton and Charlie Austin secured a straightforward 2-0 win for Sky Bet Championship leaders QPR, whose seventh consecutive clean sheet equalled a club record.
Barton scored after only four minutes and striker Austin netted from the penalty spot to put Harry Redknapp’s side firmly in control.
They surprised their opponents with a change of formation that had Middlesbrough on the back foot from the opening whistle.
Boss Redknapp opted for a 4-5-1 system with recent signing Niko Kranjcar, who was outstanding on his home debut, drifting in from the left.
It caused Boro problems immediately, although the early opener was created on the opposite flank.
Danny Simpson’s right-wing cross was not dealt with and the ball broke to Barton, who fired through a crowded penalty area from near the edge of the box.
QPR continued to dominate and the home fans wanted a penalty when Alejandro Faurlin went down under a challenge from Frazer Richardson while attempting to collect Austin’s pass.
Jason Steele then produced a good save to deny Barton – and was unlucky in the build-up to Rangers’ second goal, which arrived 10 minutes before the break.
The Boro keeper kept out Austin’s shot and the loose ball dropped to Gary O’Neil, whose follow-up was handled by Ben Gibson.
Austin duly stepped up to net his second penalty in as many matches, and struggling Boro – now without a win in seven matches – never looked like recovering.
They did rally early in the second half and substitute Lukas Jutkiewicz’s shot brought a save from in-form QPR keeper Rob Green.
Albert Adomah was just unable to connect with Jutkiewicz’s right-wing cross and later poked wide from 10 yards out as Tony Mowbray’s men at least managed to create openings.
Otherwise, it was all Rangers and O’Neil had two efforts saved by Steele before curling wide from 20 yards.
Kranjcar’s classy display earned him a standing ovation when he was substituted late on and suggested the Croatian will be a key player for the London club as they pursue an immediate return to the top flight.
They are currently well on course and remain the only unbeaten side in the second tier.
The only note of concern for Redknapp, who is already without sidelined centre-back Nedum Onuoha, will be an apparent injury to skipper Clint Hill.
Defender Hill limped off with 12 minutes remaining after appearing to pick up a knock.
QPR (2) 2 Middlesbrough (0) 0
QPR: Green,Simpson,Dunne,Hill (Ehmer 78), Assou-Ekotto, O’Neil, Barton, Faurlin (Henry 79), Kranjcar (Hoilett 83), Carroll, Austin.
Subs Not Used: Chevanton, Traore, Jenas, Murphy.
Goals: Barton 4, Austin 35 pen.
Middlesbrough: Steele, Richardson, Woodgate (Parnaby 46), Gibson, Friend, Butterfield (Smallwood 67), Leadbitter, Varga (Jutkiewicz 46),Whitehead, Adomah, Kamara.
Subs Not Used: Hoyte,Andrew Halliday,Carayol,Leutwiler.
Booked: Whitehead, Gibson, Adomah.
Ref: Darren Deadman (Cambridgeshire).