Antoine Griezmann's penalty just before the break put Atletico in control but Morata headed in his seventh goal in eight games for Chelsea before Michy Batshuayi struck with the final kick of the game.
The dramatic finish gave the Blues two wins from two Champions League Group C games ahead of a double-header against Roma.
'Today was a very important test against a side that have reached the Champions League final in the last few years,' Morata told BT Sport.
'We took the three points and now we can go home, relax and use the same mentality in the Premier League. It was a massive victory.'
Morata, who played for Atletico's cross-city rivals Real, admitted he took satisfaction from becoming the first European opponent to score a goal at their new home.
He added: 'It is always a good feeling to score the first goal in a new stadium. I am very happy.
'It is great to play with a player like Eden Hazard. He is one of the best in the world and I am very lucky to play with him.
'I am happy with my start but the most important thing is the team and winning the game.'
Antonio Conte was delighted with his side's performance, with Hazard earning special praise.
'Our performance was very good so I am very pleased for my players,' said the Chelsea boss.
'When you go 1-0 down it's very difficult to come back but we continued to play very well in the second half and concentrated well. We deserved to win.
'I think we prepared for the game very well. My players showed me great desire, will and concentration. They showed we deserved to play these types of games.
'We must be very happy because Eden Hazard's performance was amazing and it was the first big game for him after his injury. His answer was fantastic and positive.'
Hazard deflected attention onto the men that fired Chelsea to victory.
He said: 'We are very happy. It was a tough game against one of the biggest teams in Europe. We deserved to win the game.
'He (Batshuayi) scores every time he gets on the pitch! He is a top scorer so I am very happy for him. Alvaro Morata too.'
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