The Blues had an electric start to the Group H encounter with Andreas Christensen giving them the lead after nine minutes with his first goal for the club.
Lukaku then won the penalty in the lead-up to the hosts' second, but couldn't continue after hurting his ankle when hauled down in the area.
Shortly before half-time, it was a double whammy for Tuchel with Werner forced off with a hamstring problem.
It remains to be seen just how serious the injuries to Lukaku and Werner are but Tuchel will no doubt be sweating on the fitness of his two attackers, who are most accustomed to playing in the number 9 role at Chelsea.
Lukaku joined for a club £97.5milliion from Inter in the summer and already has four goals to his name on his return to the club.
The Belgian was replaced by Kai Havertz, whilst Callum Hudson-Odoi came on for Werner.
Despite their injury problems, it was a brilliant first half from Chelsea, who had a very strong XI for the Stamford Bridge clash.
Christensen guided home a volley in style to put the hosts in early control - his first goal for the club in his 137th appearance for the Blues.
And Jorginho doubled the dominant home side's lead from the spot to put the clash firmly in Chelsea's control.
Kai Havertz settled the tie with a sublime chip over the keeper shortly after half-time before Jorginho got his second of the game from the spot after Antonio Rudiger won a penalty.