Chelsea blew their chance to finish top of Champions League Group H as Magomed Ozdoev's stoppage-time equaliser forced the holders to settle for a dramatic 3-3 draw at Zenit Saint Petersburg on Wednesday.
Thomas Tuchel's side had already qualified for the last 16 and were hoping to take first place to theoretically secure an easier draw in the knockout stages.
They were just seconds away from achieving their aim when Ozdoev fired home to leave Chelsea two points behind group winners Juventus.
Werner had put Chelsea ahead after 84 seconds with his club's fastest ever Champions League goal.
Claudinho equalised and Sardar Azmoun handed Zenit the lead before half-time.
Romelu Lukaku, making his first start since suffering an ankle injury against Malmo in October, equalised with his first goal in 11 club games since the Chelsea striker netted against Zenit in September.
Werner looked to have won it with five minutes left, but Ozdoev's last-gasp goal added to Tuchel's mounting problems.
After Chelsea's damaging 3-2 defeat at West Ham knocked them off the top of the Premier League on Saturday, this was another setback for the Blues.
A long flight and temperatures well below zero made it a gruelling trip for a team already running on fumes and a return trip to Saint Petersburg for the Champions League final in May must seem a long way off for Tuchel's spluttering team at present.
Chelsea will face one of Ajax, Real Madrid, Bayern Munich or the winner of the Lille, Salzburg, Sevilla and Wolfsburg group in the last 16.
With N'Golo Kante still absent due to a knee injury, Jorginho unavailable because of a nagging back problem and Mateo Kovacic testing positive for the coronavirus this week, Chelsea's midfield was in tatters.
Tuchel made eight changes from the West Ham game, with Edouard Mendy replaced by Kepa Arrizabalaga after the Chelsea keeper's costly mistake against West Ham.
Reece James, in superb form at right wing-back this season, was deployed in central midfield as Tuchel looked for a solution to his problems in that area, but the defender was a fish out of water for much of the game.
Saul Niguez has endured a difficult start following his loan switch from Atletico Madrid, but the Chelsea midfielder finally provided a positive contribution in the second minute.
Making a lung-bursting run from his unfamiliar left wing-back role, Saul's shot was pushed away for a corner by Zenit keeper Mikhail Kerzhakov.
From Ross Barkley's resulting set-piece, Andreas Christensen flicked on to Werner and he had the simple task of poking home from virtually on the goal-line.
So often this season, Chelsea have taken the lead without killing the game off and once again they were caught out in the 38th minute.
After Chelsea failed to clear their lines, Douglas Santos's cross found the visitors' defence flat-footed and Claudinho took full advantage with a glancing header past Kepa.
There was worse to come for Chelsea three minutes later.
Barkley surrendered possession too easily in midfield and Malcom's pass split the Chelsea defence, with Azmoun beating the flimsy offside trap and rounding Kepa before slotting into the empty net.
Chelsea were in disarray at the back and it took good saves from Kepa to repel Azmoun's strike and then Malcom, who threatened with a curler in the second half.
Largely anonymous for the first hour, Lukaku grabbed Chelsea's equaliser in the 62nd minute.
Werner ran onto Barkley's pass and Lukaku was just onside as he converted the German's pass from close range.
Chelsea kept plugging away and looked to have won it in the 85th minute when Werner took Christian Pulisic's pass and drilled a low finish past Kerzhakov from 12 yards.
But there was a sting in the tale as Ozdoev lashed home from the edge of the area four minutes into stoppage time.