Visiting supporters reacted with anger to going a goal and a man down midway through the first half, causing a 10-minute stoppage at the Red Bull Arena
The issue began shortly after Jonatan Soriano had put the hosts into the lead on 22 minutes, with Basel captain Marco Streller going over to a section of the travelling support in an effort to calm them down as objects began to be thrown onto the pitch.
However, on the half-hour mark the referee called a temporary halt to the match as the away fans continued to aim projectiles at the Salzburg players as well as let off flares and smoke bombs in the stands, with both sides taken off down the tunnel.
After roughly a 10-minute stoppage - in which the home fans were in good voice despite the stop in play - the referee brought the players back out to continue the last-16 second leg.
Marco Streller and Gaston Sauro scored in the second half to complete a shock turnaround for the visitors - who had played with 10 men most of the match in a topsy turvy tie, with the hosts guilty of missing a number of chances before they also had a player sent off.
The opening leg was a 0-0 stalemate in Switzerland, meaning the Austrians were eliminated at the Red Bull Arena.
Basel, who were fined €30,000 by Uefa after failing to stop a Greenpeace protest during a Champions League encounter with Schalke earlier this season, could well find themselves in hot water with European football's governing body again after Thursday's incident.