Played in Rome’s Olympic Stadium instead of Portugal for Covid-19 reasons, the Gunners were the better side but failed to take a number of first-half chances before falling behind soon after the break.
Emile Smith Rowe was adjudged to have handled in blocking Diogo Goncalves’ cross, leading to a penalty that Pizzi converted to take his goal tally to a tournament-high of seven.
However, the lead lasted just two minutes as Cedric Soares’ low cross was converted from close range by England winger Saka.
Fresh from scoring a hat-trick against Leeds in the Premier League, Pierre-Emerick Aubameyang had two big chances but inexplicably side-footed wide from close range with the score at 0-0 and then dragged an effort off target at 1-1.
In positive news for the Gunners, left-back Kieran Tierney and forward Gabriel Martinelli made welcome returns from injury as second-half substitutes.
Saka now has six goals this season for Arsenal, with Thursday’s his first in this season’s Europa League.
The second leg is in Athens in a week’s time, sandwiched between two big league fixtures for the Gunners – the visit of Manchester City to the Emirates and a trip to Leicester.