Thomas Tuchel's side had already certified for the ultimate 16 and have been hoping to take first area to theoretically steady an less complicated draw within the knockout levels.
They were simply seconds faraway from achieving their goal while Ozdoev fired home to go away Chelsea two factors behind institution winners Juventus.
Werner had positioned Chelsea beforehand after eighty four seconds along with his club's fastest ever Champions League intention.
Claudinho equalised and Sardar Azmoun passed Zenit the lead earlier than half-time.
Romelu Lukaku, making his first begin given that struggling an ankle harm in opposition to Malmo in October, equalised with his first goal in eleven membership games since the Chelsea striker netted in opposition to Zenit in September.
Werner appeared to have received it with five mins left, but Ozdoev's ultimate-gasp intention delivered to Tuchel's mounting troubles.
After Chelsea's destructive three-2 defeat at West Ham knocked them off the top of the Premier League on Saturday, this became some other setback for the Blues.
A lengthy flight and temperatures properly beneath 0 made it a gruelling ride for a team already walking on fumes and a go back journey to Saint Petersburg for the Champions League final in May should seem an extended way off for Tuchel's spluttering group at gift.
Chelsea will face considered one of Ajax, Real Madrid, Bayern Munich or the winner of the Lille, Salzburg, Sevilla and Wolfsburg group within the final 16.
With N'Golo Kante nevertheless absent due to a knee harm, Jorginho unavailable because of a nagging returned problem and Mateo Kovacic checking out effective for the coronavirus this week, Chelsea's midfield became in tatters.
