Spain lead Group G by three points from Italy and one win from their final two games is likely to be enough to qualify automatically for next year's tournament in Russian Federation.
Morata moved to Chelsea to replace Diego Costa after Antonio Conte informed the Spain global that he is surplus to requirements at Stamford Bridge.
"It's a muscular problem".
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I don't think it's a serious problem because he stopped before it will become a serious injury. He said he would prefer to stop and not risk a bad injury.
Since joining from Real Madrid for £57million in the summer, Morata has scored seven goals for Chelsea and quickly established himself as one of the club's key players.
Spanish Football Federation have confirmed that Morata has suffered a grade two hamstring tear which is expected to keep him out for at least the whole of October 2017 and could be longer. "The national team doctors has underwent a scan on Alvaro Morata at the University Hospital Sanitas La Moraleja (Madrid) where the mentioned muscle injury has been detected".
The injured trio have been replaced by 36-year-old Athletic Bilbao striker Aritz Aduriz, Real Sociedad full-back Alvaro Odriozola and Las Palmas midfielder Jonathan Viera.