Spain host Albania in Alicante on 6 October before travelling to Israel three days later - with Julen Lopetegui's side needing four points from their final two games to confirm qualification for Russian Federation 2018.
Morata moved to Chelsea to replace Diego Costa after Antonio Conte informed the Spain worldwide that he is surplus to requirements at Stamford Bridge. I don't think it's serious. "I don't know. The doctor in the next few days will check the situation but I don't think he will be available for the national team".
Morata was taken off after just 35 minutes as Chelsea fell to a 1-0 home defeat to City who extend their lead over the Blues at the top of the Premier League table to six points after seven games.
It was initially thought that Morata would be able to return to action after the global break, but the Spanish Football Federation have confirmed that the 24-year-old suffered a grade two hamstring tear that will likely keep him out for all of October plus two weeks into November.
The 24-year-old, who joined Chelsea from Real Madrid during the summer, is one of three players Spain coach Julien Lopetegui wlll be without for the two games.
Chelsea will now monitor Morata's recovery and hope that he is fit to face Crystal Palace on October 14.
Real Sociedad right-back Alvaro Odriozozla and Las Palmas midfielder Jonathan Viera will fill the voids left by the unavailable pair.