Legia on Tuesday beat the Estonian team 1-0 away in the second leg of their Champions League round two qualifier.
The Polish side’s Portuguese striker Rafael Lopes scored the only goal of the match in Tallinn in the 67th minute.
Legia defeated Flora 2-1 in the first leg of their Champions League round two qualifier last week.
The Polish champions will now face Croatian side Dinamo Zagreb in the third round of Champions League qualifiers.
To qualify for the Champions League group stage, Legia need to eliminate Dinamo Zagreb and one other rival, Poland's PAP news agency has reported.
Legia in May won the Polish premier league championship for the 15th time.
Legia Warsaw players with coach Czesław Michniewicz (centre) during a training session last month. Photo: PAP/Leszek Szymański
The Polish side qualified for the group stage of the 2016/2017 Champions League and drew 3-3 with Spain's Real Madrid in November 2016.
Legia later that month lost 4-8 to German side Borussia Dortmund in the highest scoring match in Champions League history.
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Source: PAP