The Pride Of London had earlier won the first leg 1-0 thanks to a spectacular overhead kick goal by Oliver Giroud.
Tuchel went for a front three of Hakim Ziyech, Timo Werner and Kai Havertz and the three combined for Chelsea’s first goal.
Ziyech finished off from a Werner cut back pass to give the hosts the lead.
Chelsea nullified Atletico Madrid’s goal threat by keeping Luis Suarez and co quiet.
Substitute, Emerson put the icing on the cake with a goal in the closing moments of the game with his first touch.
The Draws for the quarter final will be made on Friday.
Meanwhile, Bayern Munich also defeated Lazio 2-1 in Germany to seal a place in the quarter finals thanks to goals from Robert Lewandoski and Choupo Moting.