A match that for an hour was completely devoid of the kind of flashpoints that marred October's Premier League meeting suddenly had one when Clint Hill was harshly adjudged to have bundled over Daniel Sturridge.
Mata stepped up to score the only goal of a game dominated by the reunion between Chelsea captain John Terry and Rangers defender Anton Ferdinand, neither of whom put a foot wrong following what had been the most combustible of build-ups.
The match itself was always going to struggle to live up to the drama that preceded it, which culminated in full body searches for fans entering the ground and the cancellation of the traditional pre-match handshake.
The former was prompted after police on Friday night confirmed they were investigating allegations Ferdinand had received "malicious communication", although they refused to reveal whether it contained a bullet.
Ferdinand and Terry were spared having to shake hands with each other after the Football Association agreed the clubs did not have to undertake the traditional pre-match ritual.
Ferdinand had reportedly been agonising over whether to accept Terry's hand four days before the court case begins in which the Chelsea and England captain stands accused of racially abusing his fellow defender.
Terry denies the charge, which relates to an altercation between the pair in October's league clash at Loftus Road.
But that did not prevent him being jeered every time he touched the ball today, while he was also the victim of numerous abusive taunts.
Chelsea fans refrained from using the notorious "Anton Ferdinand, you know what you are" chant that they were warned would see them punished, although they did sing "Anton, what's the score?" after the visitors took the lead.
Both sets of supporters cranked up the decibel level before kick-off but had little to cheer in a disappointing first half that saw only one shot on target.
That came after Mata, playing more centrally in the absence of Frank Lampard, pounced on a Luke Young slip in the 12th minute and unleashed a 15-yard drive too close to Paddy Kenny.
Otherwise, the final ball from both sides was sadly lacking, meaning a succession of speculative efforts that were well off target.
A fixture that had seen Chelsea reduced to nine men in October was also a more controlled affair and it was almost half an hour before Mike Dean brandished the first yellow card for a Shaun Wright-Phillips foul on Raul Meireles.
Ramires should have done better with great cutback opportunity after being released by a wonderful Mata backheel but neither side deserved to be ahead at half-time.
QPR threw on Federico Macheda for Heidar Helguson at the restart but it was Chelsea who flew out of the blocks, with Fitz Hall booked for handball before Sturridge lashed over after great work from Fernando Torres.
But the game really exploded into life on the hour mark.
Petr Cech parried a Wright-Phillips cross just too far in front of the outstretched foot of Jamie Mackie and Chelsea surged down the other end and won a penalty.
QPR were furious at the award but Mata shrugged off the jeers to score, the midfielder celebrating with most of his team-mates in front of the visiting fans. Terry was a notable absentee.
Ashley Cole was carded for fouling Wright-Phillips before Chelsea lost Ramires to a serious-looking injury.
The midfielder appeared to twist his ankle blocking a shot and - after several minutes' treatment - was carried off on a stretcher to be replaced by Oriol Romeu.
QPR had already thrown on Rob Hulse, who was denied a penalty in the dying minutes.
And there was a flashpoint deep into stoppage-time when Romeu was booked for diving in on Hulse, with Young almost snatching a draw when his 20-yard drive was parried by Cech.