After Andreas Christensen scored his first Chelsea goal in his 137th appearance for the club, Lukaku had to go off with an apparent ankle injury after winning a penalty that was fired home by Jorginho.
Kai Havertz replaced the Belgium international and, after Werner was substituted due to a hamstring issue, increased their lead early in the second half.
Ballon d'Or nominee Jorginho converted another spot-kick to round off the scoring before the hour mark, though Chelsea remain three points behind group leaders Juventus after the Italian side left it late to beat Zenit 1-0.
The offside flag spared Werner's blushes after a miskick inside the six-yard box but Chelsea were soon ahead when Christensen volleyed fellow centre-back Thiago Silva's cross into the top-right corner.
Chelsea was awarded a penalty when Lasse Nielsen scythed down Lukaku in the box and Jorginho confidently sent his spot-kick straight down the middle.
The Blues suffered another injury blow before half-time with Werner appearing to pull his hamstring while sprinting into the box to support Havertz.
Havertz was unable to take that opportunity but he got the better of Ismael Diawara – who replaced goalkeeper Johan Dahlin at half-time – three minutes after the restart, dinking fellow substitute Callum Hudson-Odoi's pass in off the post.
Referee Francois Letexier pointed to the spot again after Eric Larsson bundled Antonio Rudiger over in the box and Jorginho once more produced an unerring finish.
Tuchel took the chance to give N'Golo Kante, Cesar Azpilicueta and Ben Chilwell a rest in the closing stages, with Chelsea seeing out a resounding victory at a canter.