Raków cruised to a 4-0 victory over Malta's Valletta FC in Ta' Qali on Thursday to complete a comfortable aggregate win after taking the first leg 3-1 at home.
GKS Katowice overturned a one-goal first-leg deficit by defeating Slovakia's MSK Žilina 3-1 at home.
The Polish side had lost the opening match 2-1 in Slovakia.
In the third qualifying round, Raków will face Sweden's Hammarby IF, which dropped into the Conference League qualifiers after losing its Europa League qualifying tie against Belgium's Anderlecht.
GKS Katowice will take on Israel's Hapoel Tel Aviv, which eliminated Bulgaria's Ludogorets Razgrad.
The third-round matches are scheduled for August 6 and 13.
Both Polish sides will need to progress through the fourth playoff round to reach the league phase of the UEFA Conference League.
On Wednesday, Polish clubs Lech Poznań and Górnik Zabrze were both eliminated in the second qualifying round of the Champions League.
Both dropped into the third qualifying round of the Europa League, where Lech will face KÍ Klaksvík of the Faroe Islands and Górnik will play Hungary's Ferencváros.
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Source: IAR, PAP