Antonio Conte stated on Saturday that the decision to remove Morata had been precautionary, but the Blues could now face up to a month without their star striker.
According to the Spanish Football Association, the former Real Madrid man suffered a grade two hamstring tear, which has also caused him to pull out of international duty.
A huge blow for Conte who could see Morata sidelined for over four weeks. As well as Spain's World Cup qualifiers, the 24-year-old would miss two Champions League games against Roma, and Premier League clashes against Crystal Palace, Watford, Everton and Bournemouth.
Morata had scored seven goals in nine appearances in all competitions for the Blues since joining from Real in the summer, and will now be sorely missed for a vital chunk of Chelsea's season.