Willian struck an 89th-minute winner as Chelsea beat Everton 1-0 but the Premier League leaders could face disciplinary action once more after Branislav Ivanovic appeared to headbutt James McCarthy.
The flashpoint occurred after Nemanja Matic thought he had scored four minutes from time, only for the deflected strike to be ruled out for offside against Ivanovic, with the ball deflecting off the Serbia international's shoulder and past Everton goalkeeper Tim Howard.
Tempers flared when Gareth Barry then tripped Willian, earning a second yellow card, and Ivanovic motioned his head towards McCarthy in the resulting fracas.
The Everton substitute was booked for his part in the melee, but Ivanovic avoided censure from referee Jonathan Moss and could face retrospective action from the Football Association.
There was still time for Willian to net after Howard was unconvincing in clearing a cross as Chelsea remained seven points clear of Manchester City.
It could have gone either way until a frantic final four minutes.
The suspended Diego Costa scored twice in August's 6-3 win at Goodison Park and would have relished the chances created by Chelsea, but the Blues struggled to test fit-again goalkeeper Howard.
Instead it was Petr Cech who had to show his enduring quality after being selected ahead of Thibaut Courtois.
He twice saved from Romelu Lukaku, the second time when the former Chelsea striker was four yards out, and Mourinho made a point of going to Cech at full-time.
Mourinho, who was last month fined £25,000 for saying there was a ``clear campaign'' against Chelsea, continues to imply his side are unfairly treated and two decisions went in favour of Everton in the opening quarter of the contest.
Chelsea might have had a fourth-minute penalty when the ball hit Steven Naismith's arm and Everton had another reprieve when Barry fouled Juan Cuadrado and Eden Hazard in quick succession, but was booked only for the first offence.
The FA Cup loss to Bradford gives Chelsea a rare weekend off and Costa will be available for next Tuesday's Champions League last-16 clash at Paris St Germain following his disputed three-match suspension, before returning to aid the title tilt.
Cuadrado made his full debut in a Chelsea side showing four changes following the win at Aston Villa, including a surprise switch in goal.
Whether Courtois was rested or dropped was unknown, but Cech, on his fourth Premier League start this term, saved well with his foot from Lukaku after eight minutes.
Chelsea had already had chances before then, the first when the peerless Matic showed force and finesse before drilling a 25-yard shot over.
Cuadrado had an effort blocked soon after and the ball ricocheted back towards Naismith.
The Scot appeared to move his right arm towards the ball, to block it with his upper arm from Cuadrado, but Moss was unmoved, much to the chagrin of Mourinho.
Willian, playing centrally with Oscar absent as a precaution, cut in from the left before curling over.
Then Barkley fed Lukaku, whose determination to impress on a stage where he found chances limited saw him snap at his shot as Cech saved.
Barry shot wide soon afterwards, but then it was all Chelsea.
Cuadrado fired wide across goal and Howard, after eight matches out with a calf problem, saved Loic Remy's header.
Cesar Azpilicueta was booked for a foul on Aaron Lennon, who was making his full debut after his loan move from Tottenham, as Everton played mainly on the counter.
There were few chances to break, though, and any forays forward were snuffed out by the excellent Kurt Zouma.
Remy fired wide before Moss showed leniency towards Barry, who was booked for a foul on Cuadrado and tugged Hazard, only to avoid a second yellow and a red.
Besic, another candidate for a second yellow, was replaced by McCarthy at half-time.
Hazard was felled by Seamus Coleman, who was duly booked, and then stung the hands of Howard with a near-post effort.
Howard saved a Matic free-kick and then a curling Willian effort before Everton, and Lukaku, had a glorious opportunity.
Bryan Oviedo's cross found Lukaku four yards out and opposed only by Cech, who saved at point-blank range.
Matic thought he had won it four minutes from time, but Ivanovic impeded Howard's view and the officials ruled in Everton's favour.
Then Barry flicked out a leg to fell Willian and Chelsea players surrounded Moss calling for the midfielder's dismissal.
Ivanovic, McCarthy and Jon Stones were particularly physical with each other, and the Chelsea right-back could now be facing a ban for his over-zealous actions.
There was a sting in the tail for Everton as Howard failed to punch clear and Willian drilled in the winner.