Werner has been out of favour at the Stamford Bridge since the arrival of Romelu Lukaku from Inter Milan towards the closure of the summer transfer window.
He had not started a game since the opening day victory against Crystal Palace at Stamford Bridge in August.
The former Leipzig man gave Chelsea the lead against the Villans on 54 minutes but Cameron Archer pulled parity for the visitors.
Chelsea went on to win 4-3 on penalties to book a date with another Premier League rivals Southampton in the fourth round of the competition.
“It’s good to be back on the score sheet, good to score at Stamford Bridge and I’m happy that I’m back on the pitch,” the club’s official website quotes Werner.
“I think that the last few weeks were not very easy for me, but every goal, every assist brings me back on track, so it was good for me today and also for the team.”
The German reacted on the game: “I think both teams gave everything. Aston Villa were a very tough opponent and they showed why they are always very hard to play against.
“I think in the second half we were lucky to score an early goal, it gave us a little bit of a push, but 10 or 15 minutes after the goal we lost a bit of control when we conceded.
“After that we wanted to finish the game in 90 minutes, it was important. In the end it didn’t happen, but good penalties at the end saved us.”
