Raków's Ukrainian midfielder Vladyslav Kochergin scored the only goal of the match at the Municipal Stadium in the southern Polish city of Częstochowa in the 54th minute as the two sides began their European campaign on Tuesday.
Raków will play Flora in the second leg next Tuesday, July 18, in Tallinn.
The winner of the two matches will go on to face either Azerbaijani side Qarabag Agdam or Gibraltar's Lincoln Red Imps in the second round of Champions League qualifiers, Polish state news agency PAP reported.
The loser will be relegated to the lower Europa Conference League.
To qualify for the Champions League group stage, Raków need to eliminate Flora Tallinn, Qarabag Agdam/Lincoln Red Imps and two other rivals.
Raków in May won the Polish premier league championship for the first time, while heavyweights Legia Warsaw, the most successful Polish football club in history, finished runners-up.
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Source: IAR, PAP
