The Swans head coach acknowledged the decisive moment should not have stood, even as his side claimed victory in west London.
“It was outside the box, not a penalty,” said Matos after the victory had given his team back-to-back away wins for the first time this season and took them up to 10th place in the Championship.
When Tylon Smith brought down Eom Ji-Sung, the contact occurred outside the area, yet referee John Busby pointed to the spot.
Zan Vipotnik made no mistake, converting his 24th goal of the season to double Swansea’s lead.
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That late decision proved crucial in a game that had already swung in Swansea’s favour inside the opening minutes, when Steve Cook endured a nightmare start to his final appearance for QPR.
The veteran defender, captaining the side in his 100th outing for the club, was caught out less than two minutes in.
Attempting to clear Melker Widell’s hopeful delivery, Cook instead collided with team-mate Rhys Norrington-Davies, allowing Ronald to race through and calmly finish past Joe Walsh.
It was a gift that handed Swansea early control, something Matos felt his team used effectively.
“We started really well, dictating with the tempo we wanted with the ball and with the pressing as well. It was quite good to see.
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“Queens Park Rangers are a good team with good organisation who use the width of the pitch really well, so there was a lot of effort from us, really nice to see, and it was a well-deserved win.”
"I think that's the best way to sum it up, it was a really mature performance," he said.
“Maybe there were periods of the game where we could have had more control with the ball in order to find the players at the right moments in the right areas, but I think this is normal when we are in this moment of the season.
"For the future that is something we will want to improve, but we also created some good chances to score and we could have had a few more goals.
"So I am pleased, we just need to keep pushing now. We have one more away game, which we know is a very long way for us, and a home game so let's see how we can finish."
QPR attempted to respond after the early setback, but struggled to find rhythm in the first half.
Rumarn Burrell set up Rayan Koli for a chance that drifted wide, while Isaac Hayden forced a strong save from Lawrence Vigouroux and Kieran Morgan fired over.
Swansea might have extended their lead before the interval, only for Walsh to produce a sharp double stop to deny Sam Parker and then Adam Idah on the rebound.
The pattern continued after the break, with Walsh again called into action to keep out Goncalo Franco and Idah, while at the other end Harvey Vale curled a free-kick just over.
Cook, despite his early error, was given a warm ovation when substituted on the hour mark, but the contest turned decisively in the closing stages with the controversial call.
QPR boss Julien Stephan was left frustrated by both the initial mistake and the key decision that followed.
"I think the way we concede the first goal after two minutes – we gave them the goal – it has an impact on how we played in the first half. We didn't play enough forward, we didn't take enough risk with the first pass.
"It was better in the second part of the game. Of course the penalty had a huge impact. It's unbelievable to concede a penalty like this – I don't know how it's possible.
"But I want to highlight the reaction of the players after this. Even with the decision, the second goal conceded, they tried to give everything to score one goal and the second one."
Norrington-Davies did pull one back in stoppage time, reacting quickest after Paul Smyth struck the crossbar, but it came too late to change the outcome.
In the end, Swansea left with the points — but even their own manager conceded the big moment had gone in their favour.
