Visiting supporters reacted with anger to going a goal behind midway through the first half, causing a 10-minute stoppage in Salzburg.
The issue began shortly after Jonathan had put the hosts ahead 22 minutes in, with Basel captain Marco Streller going over to the traveling section of Basel supporters to try to calm them down.
However, on the half-hour mark the referee blew a halt to the match as the away fans continued to bombard the pitch and Salzburg players with projectiles, deeming the players to be endangered by the disruption.
After roughly a 10-minute stoppage — in which the home fans were in good voice despite the stop in play as their team held the slender lead — the referee brought the players back out on to the pitch to continue the Europa League last-16 second leg.
The opening leg was a 0-0 stalemate in Switzerland, giving the upper hand to the Austrian hosts ahead of the Red Bull Arena tie.