The German international, who has had a torrid time in front of goal since joining from Red Bull Leipzig last summer, gave the Blues the lead with a well-timed header, only for Villa to equalise through teenager Cameron Archer, sending the tie to spot-kicks.
Chelsea won 4-3 on penalties to progress in the competition and have been awarded a home tie against Southampton in the fourth round.
Werner, who didn’t step up to take any of Chelsea’s five penalties, admitted that he had picked up a knock and chose not to take one.
‘I had some pain in my calf but with only three substitutes, I couldn’t go off,’ he said after the win.
‘But when you have fit players on the pitch, it’s better they shoot than me today.’
Speaking before the match on Wednesday night, Chelsea boss Thomas Tuchel insists he still believes Werner will come good at Stamford Bridge, despite calls from many sections of the fan base for the club to sell the 25-year-old.
‘He gave us a clear impression of how dangerous he and Romelu can be together,’ Tuchel said.
‘The stuff that you don’t see, in training sessions, he’s more relaxed, more fluid in his movements, with more confidence.
‘That’s why he came on early against Tottenham, there are clear signs he is in a good way and he can prove it tomorrow.
‘Timo was in better positions and we had him in dangerous positions around Romelu. And he got an assist… he moves smart, he’s free and his decision making is with more confidence… Hopefully he can push himself and keep that momentum going.’
Chelsea, who are unbeaten in the Premier League so far this season, play host to champions Manchester City on Saturday, hoping to continue their fine start to the campaign.
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