Despite dominating both territory and possession it took the second-half arrival of substitute Eden Hazard to add spark to a Chelsea team frustrated for long periods.
And Spaniard Morata, who had earlier missed a glorious chance, capitalised on some extra space by sweeping in Willian's flick from a Cesc Fabregas pass.
The hosts were unable to add to their lead and had goalkeeper Kepa Arrizabalaga to thank for preserving the three points when he turned away Istvan Kovacas' drive late on.
The result ensured the 2013 Europa League winners top the group with six points, having beaten PAOK Salonika in Greece in their opening fixture last month.
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EUROPA LEAGUE