The match will kick off at Olympiakos Piraeus' home ground in the Greek capital on 25 February.
The game, which was due to be held at the Emirates Stadium, was moved because Portugal is on the UK's 'red list', which means those arriving from the country must self-isolate for 10 days, with no exemptions for elite athletes.
The first leg will be held in Rome's Stadio Olimpico.
Manchester United's Europa League last-32 game at Real Sociedad was moved from San Sebastian to Turin due to Covid-19 travel restrictions in Spain that prevent the English side from entering the country.
Liverpool's Champions League first leg away to RB Leipzig on 16 February has been moved to Budapest as a result of travel restrictions in Germany, as has Manchester City's first leg at Borussia Moenchengladbach on 24 February.