While Pavlidis's winner in the fourth minute of stoppage time sparked wild celebrations among the Greek fans, England standin manager Lee Carsley got a sobering reality check.
Two victories since Gareth Southgate stood down had raised Carsley's stock as a likely full-time option, but after a ragged defeat at the hands of Greece, his hopes may have dwindled.
Pavlidis had given his side the lead early in the second half with a clinical finish and Greece had three goals ruled out against an England side that started with an ultra-attacking line-up but misfired badly.
Jude Bellingham looked to have rescued his side when he lashed home an 87th-minute equaliser but there was another twist as the outstanding Pavlidis punished more woeful defending to shoot past Jordan Pickford from close range.
Greece top the table with a maximum nine points while England's first defeat under Carsley left them second with six.
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