Valentino Lazaro's 73rd-minute goal meant the team took an unassailable 12-point lead over Austria Vienna, who beat basement club Ried 3-0, with three matches to play.
Salzburg have dominated the Bundesliga since sponsors, energy drinks manufacturer Red Bull, became involved with the club in 2005.
However, many supporters abandoned the club in protest when they changed their traditional purple kit for Red Bull's corporate colours, and founded a new club, Austria Salzburg, which is now in the third tier.
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Saturday's match was watched by just over 15,000 fans.
UEFA have not yet confirmed whether Salzburg and German Bundesliga side RB Leipzig, who are owned by Red Bull and have also qualified for the Champions League, will both be able to enter the competition.
European soccer's governing body has said it will study the management structure of the two clubs when the entry list for the competition is complete.
Leipzig's general manager, Oliver Mintzlaff, told German media that the company had done its homework and that both teams were eligible to take part under UEFA rules.
Salzburg, who will enter at the second qualifying round next season, have not qualified for the Champions League group stage since Red Bull became involved. (Writing by Brian Homewood in Berne,; Editing by Neville Dalton)
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