The Dutch coach, who was previously Jurgen Klopp's right-hand man at Anfield, leaves the club after less than six months in charge.
Salzburg confirmed their decision on Monday, two days after Lijnders had secured a 3-0 home win over Austria Klagenfurt.
In a joint-statement, 'many unsatisfactory performances' were cited as a reason for Lijnders' dismissal.
Chief executive Stephan Reiter and sporting director Rouven Schroder explained: "We began recently to analyse, as planned, what has unfortunately not been a satisfactory season so far.
"It was clear to see that in many of our matches we have been far short of our own requirements and aims.
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"We have therefore become convinced that our team needs a new impulse under new management, even if we continued to hope for a turnaround until the end.
"We would like to thank Pep for his work. He put a lot of effort and passion into it and has provided important momentum for our further development.
"We are now very intensively looking for a new coach and will communicate as soon as a decision is made. We clearly want to start training again on January 3, 2025 with our new coach in place."
It had been Lijnders' first managerial role since a four-month stint in charge of Dutch side NEC Nijmegen back in 2017.
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The 41-year-old spent six years as Klopp's no.2 at Anfield prior to being appointed by Salzburg in July.
Across 28 matches in all competitions, Lijnders picked up 13 wins, seven draws and eight defeats.
Those results meant his side headed into the winter break fifth in the Austrian Bundesliga.
Salzburg sit ten points adrift of league leaders Sturm Graz after 16 matches.
Meanwhile, Lijnders lost five out of his six Champions League matches at the helm, with the club 32nd in the league phase table.
His departure comes just weeks before Klopp takes up a role with Red Bull.
The former Reds boss will become Red Bull's head of global football from January 1.
Klopp has agreed a four-year deal through to 2029 following his Liverpool exit in the summer.
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As part of the role, he will work with the group's six clubs including RB Leipzig, Salzburg and Leeds.