The decision had left Stamford Bridge raging and their mood soured further when the Clarets took a deserved lead midway through the half. Defour had room in the centre of the pitch and spread the ball wide to Lowton and his cross from deep was brilliantly flicked home from 12 yards by Vokes.
It was the same combination in the action again on the hour with Heaton producing a more spectacular save to tip Alonso’s 25-yard free-kick over the bar.
The Clarets almost made it save a minute later when Brady’s 20-yard free-kick hit the post, but they managed to hold on through four minutes of stoppage time to begin the season with a stunning victory.
The Clarets landed a first opening day win in the top flight since 1973 in some style, beating Antonio Conte’s side 3-2 in a bad tempered clash.
With just under 10 minutes to go Fabregas saw red after collecting a second yellow, leaving Chelsea down to nine.
Chelsea had improved after the break and they got a goal back midway through the half. Willian was the architect, creating space on the right to clip in a cross and £70million man Morata, on as a second half substitute, glanced home his cross after peeling off the back of James Tarkowski.
Alvaro Morata briefly made things nervous as the champions tried to rally after the break, and despite being down to nine men David Luiz cut the deficit even further two minutes from time.