AZ trailed 1-0 at the time and conceded a second goal on Friday. Despite losing 2-0 at home, however, they went through on the away goals rule after winning last week's first leg 3-1 in Greece.
Thursday's blaze caused damaged estimated at 500,000 euros (426,608.17 pounds), the club's general director Toon Gerbrands told Dutch television on Friday.
The short circuit, which occurred in one of the electrical boxes for the floodlights, caused smoke and fire clearly visible to the referee, who halted the game to allow the crowd to evacuate the venue and the blaze to be dealt with.
UEFA ordered the match to be completed on Friday so that the winner would be known before the draw for the group phase of the Europa League which was being held in Monaco later in the day.
(Reporting by Mark Gleeson in Cape Town; Editing by Tom Bartlett)
