Jose Mourinho's side climbed above previous leaders Liverpool on goal difference after a sterile London derby at Stamford Bridge.
UEFA chief Ceferin's intervention came after a spate of penalties being awarded because balls have — even unwittingly — hit outstretched or raised arms.
Premier League: Diogo Jota caps Liverpool's fightback to beat West Ham; Manchester City, Chelsea also claim wins
It was Liverpool's fourth successive victory since influential defender Virgil van Dijk was sidelined for several months with a serious knee injury suffered against Everton.
Everton will head into the Merseyside derby against Liverpool after the international break with maximum points from their first four games.
Premier League: Manager Frank Lampard warns Tammy Abraham to respect rules after Chelsea crush Crystal Palace
With Chelsea leading 3-0, Abraham wanted to take their 2nd penalty of the match. Abraham and Timo Werner discussed who should have it before captain Azpilicueta intervened and took the ball out of Abraham's hands and gave it to Jorginho.
League Cup: Jose Mourinho gets better of Frank Lampard as Tottenham see off Chelsea to reach quarter-finals
Going out of the League Cup was the latest setback for Lampard, whose side has only four points from its opening three Premier League games.
Silva joined Frank Lampard's side from Paris Saint-Germain on a free transfer in August and is waiting to make his Blues debut after being granted a longer break than his new team-mates.
Premier League: Sadio Mane brace sees Liverpool beat 10-man Chelsea; Leicester City top points table after Burnley win
Mane was involved in the turning point at Stamford Bridge as the first clash between Premier League title contenders this season swung Liverpool's way.
Timo Werner marked his Premier League debut by winning a penalty that Jorginho converted to put Chelsea ahead, but the Germany star took a whack on his leg as he was tripped by Brighton keeper Mat Ryan in the incident.
Premier League: James' stunner helps Chelsea beat Brighton; Wolves makes winning start against Sheffield
After a spending spree of $250 million on some of Europe’s most exciting stars, Chelsea were indebted to a wonder strike from one of their homegrown players during a win in their opening English Premier League game.
Premier League: Chelsea manager Frank Lampard expecting extra pressure after spending spree in transfer window
Chelsea have spent nearly £200 million ($263 million) as they have brought in on Hakim Ziyech, Timo Werner, Ben Chilwell, Thiago Silva, Kai Havertz and Malang Sarr and could add even more new faces.
Sarr is seen as one for the future by Chelsea manager Frank Lampard and will be sent on loan this coming season to build his experience.
Werner, a German international, agreed a 45 million pound move to Stamford Bridge last month and has already started training with the Londoners even though he is ineligible to play until next season.
Chelsea have reached an agreement with RB Leipzig to sign striker Timo Werner, who is set to join the English side in July, the Premier League club announced on Thursday.
Bundesliga: Mainz secure victory over Borussia Dortmund; Leipzig drop points after draw against Dusseldorf
Fortuna Düsseldorf stunned Leipzig with two late goals to draw 2-2 in the Bundesliga on Wednesday and boost their hopes of avoiding relegation.
RB Leipzig forward Timo Werner set to join Chelsea after Premier League club agrees to meet his release clause
The Premier League club reportedly agreed to a deal in principle to sign Werner after meeting his release clause of around 60 million euros ($68 million), which expires on 15 June.
Bundesliga: RB Leipzig reclaims third place after win at Cologne, in line to seal Champions League spot
Leipzig are now third on 58 points, two behind second-placed Borussia Dortmund and nine off leaders Bayern Munich
Bundesliga: Timo Werner scores hat-trick as RB Leipzig rout Mainz; Schalke's crisis deepens with Augsburg defeat
Werner opened the scoring in the 11th minute, and there were more goals from Yussuf Poulsen and Marcel Sabitzer before the break. Werner grabbed two more in the second half
Champions League: RB Leipzig knock Tottenham Hotspur out of tournament; Josip Ilicic nets four to send Atalanta into quarter-finals
Playing in the Champions League for the first time this season, Atalanta’s European adventure continued in emphatic fashion as Slovenian Ilicic netted twice in each half to guide his side comfortably into the quarter-finals.