Werner surely cemented top penalty billing with the Blues by blasting two perfect spot-kicks, with former regular taker Jorginho watching on as captain on the night.
Rennes defender Dalbert conceded both penalties to end up sent off before half-time.
Where the first penalty was cast iron, the second was hotly disputed.
Dalbert had no complaints after upending Werner for the first spot-kick.
But his block on Abraham's shot deflected onto his raised arm, and that led to the second penalty – but only after a Video Assistant Referee intervention.
German referee Felix Zwayer awarded the contested penalty after a visit to the pitchside monitor, and then sent off Dalbert for a second booking for good measure.
Jorginho's second missed penalty of the season in Krasnodar handed Werner his chance to step up on spot-kicks.
Three from three and all in emphatic style now leaves the nerveless 24-year-old German at the front of Chelsea's dead-ball duties.
Werner now also boasts seven goals in his 11 Chelsea outings, following his £53million summer switch from RB Leipzig.
Kurt Zouma escaped without punishment when Nayef Aguerd's header struck his arm at the top of the night, with the Blues defender's arm down by his side.
There was no argument about Chelsea's first penalty though, with Werner tricking Dalbert into felling him in the box.
The striker stepped up and coolly slotted home, to push Chelsea into the lead just 10 minutes in.
Benjamin Bourigeaud whipped a free-kick across the face of the Chelsea goal that Mendy was relieved to watch skid to safety, after Hakim Ziyech committed a percentage play foul for a yellow card.
Chelsea pushed quickly back onto the attack, and this time the disputes were far and wide as Dalbert was penalised for handball via a VAR review.
Abraham's shot ricocheted off Dalbert's legs and onto his raised arm, and initially both sides thought the issue had passed.
But then referee Zwayer was called to the pitchside monitor, and everything changed.
First the official awarded the penalty, and then he dismissed Dalbert for a second yellow card.
Fury raged on the Rennes bench with anguished cries ringing out around the empty Stamford Bridge.
Meanwhile, Werner stepped up and rifled another perfect penalty into the top corner to make it 2-0.
Ziyech blazed over the bar to start the second half before Chelsea further confirmed control.
James' fine low cross begged for a near-post finish and Abraham delivered in some style, flicking home to extend the hosts' lead.
Replacement Olivier Giroud should have added a fourth after Ziyech's tidy through-ball, only for the goalkeeper to palm to safety.
Chelsea coasted home but still needed Mendy to pull off a smart save from Clement Grenier, to preserve his latest clean sheet.