Portugal would have likely been expecting to face Italy in the play-off final, but the European champions slumped to a shock 1-0 home defeat by North Macedonia last week.
Pandev had gone nine games without hitting the net, but his brace took Napoli past Genoa.
Gonzalo Higuain's presence in the Napoli squad served as a reminder of Arsenal's failure to recruit during the close season, with the former Real Madrid striker opting for a move to Italy ahead of a switch to the Emirates Stadium.
Napoli were missing top scorer Edinson Cavani due to suspension but with Lorenzo Insigne stepping up to the plate admirably, the visitors set their stall out early and should have had several goals in the opening half.
European and Italian champions Inter Milan have been charged by federal prosecutors for improper conduct during the acquisition of Goran Pandev from Lazio just over a year ago.