The 24-year-old limped off the pitch in the 35th minute as Chelsea were beaten 1-0 at Stamford Bridge by their title rivals thanks to a Kevin De Bruyne goal.
Chelsea and Spain's doctors have both assessed Morata's hamstring injury and the Blues will continue to do so as they aim to get him back as soon as possible.
Antonio Conte has become heavily reliant on his Spain international since signing him for £57 million from Real Madrid in the summer.
Morata has seven goals and two assists in 2017-18 and Conte described why he chose to start his striker for third match in a row after his side lost to Manchester City.
"It's normal when you play three massive games in only seven days, you must consider this aspect. We needed to take this risk because Morata for us is an important player," Conte said at Stamford Bridge.
Morata will get treatment at Cobham Training Centre while most of his Chelsea team-mates are away with their national teams. Michy Batshuayi and Eden Hazard are expected to play in Morata's role up front in his absence.
WHICH GAMES COULD ALVARO MORATA MISS?
|DATE||UPCOMING CHELSEA FIXTURES||HOME/AWAY|
|Oct 14||Crystal Palace||Away|
|Nov 5||Manchester United||Home|