Three-time Olympic champion Stoch made jumps of 121.5m and 130m, finishing just outside the top 10 at the Bergisel Ski Jump, according to news outlets.
Meanwhile, Żyła came 14th, thanks to jumps of 131m and 115m.
Two other Poles made the top 30 in Innsbruck, Aleksander Zniszczoł finishing 24th (121m, 120.5m), while Paweł Wąsek came 29th (108m, 121.5m).
Stoch, who won the Four Hills Tournament in 2017, 2018 and 2021, now sits 15th in the overall standings (752.8 points), with Żyła 18th (729.8 points), the skijumping.pl website reported.
Meanwhile, Jan Hörl of Austria won the Innsbruck event in front of 21,000 spectators at the Bergisel ski jump, thanks to efforts of 134m and 127.5m.
Japan's Ryōyū Kobayashi came second (128.5m, 132m), with Austria's Michael Hayböck finishing third (131m, 135.5m).
Kobayashi now leads the overall ranking of the 2023/24 Four Hills Tournament on 857.6 points, according to officials.
The competition now moves to Bischofschofen, Austria, for the fourth and final event at the Epiphany ski jump on Saturday.
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Source: skijumping.pl, viereschanzentournee.com, sportowefakty.wp.pl