There was chaos and confusion at Stamford Bridge as the Blues were awarded a penalty after intervention from the video referees.
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Cue anger from the Borussia Dortmund players, who were unhappy with the penalty decision against them, despite the ball clearly hitting the hand of Marius Wolf.
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Havertz stepped up to take the spot-kick having not scored since January 15, eight games ago.
His effort came back off the post and the ball was subsequently cleared by a Dortmund defender.
The German forward had his hands on his heads, but was given a repreive.
Replays showed the Dortmund defender, who cleared the ball, was already in the box before Havertz had taken the penalty, and the Chelsea man was allowed to retake.
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He coolly stepped up and put it on the same side, giving the Blues the advantage in the tie.
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That was Chelsea's second goal, after Raheem Sterling's opener, to put them 2-1 up in the tie.
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That goal controversy proved to be the decisive factor as the Blues held on to win 2-0 in the match, and progress in the tie.
It ended Dortmund's run of 10 wins in a row as they withstood intense pressure.
Graham Potter's side are now through to the quarter-finals of the Champions League.