With 10 minutes to play in the opening period, the Spain international pulled up with a hamstring injury and had to come off the field.
Morata was replaced by Willian as Antonio Conte opted for the Brazilian ahead of back-up striker Michy Batshuayi, with Eden Hazard moving to centre-forward.
The 24-year-old has been in red-hot form for Chelsea, scoring seven goals in seven appearances in all competitions this season after making a €62 million move move from Real Madrid in the summer.
If Morata is forced to miss an extended spell, Batshuayi is likely to get a run of games as he looks to show he's worthy of a starting spot.
The Belgium international has been in good scoring form for the Blues, with five goals in six appearances in all competitions in 2017-18 heading into Saturday's match.