The Poles take on Spartak Trnava in Slovakia next Tuesday in the second leg.
Legia drew criticism for making simple mistakes and for proving ineffective while trying to attack.
Spartak Trnava’s goals came from Erik Grendel in the 16th minute and from Jan Vlasko in the third minute of injury time.
Legia moved on to the second round of Champions League qualifiers after eliminating Irish side Cork City last week.
Legia in May won the Polish premier league championship for the third time in a row.
The Polish side qualified for the group stage of the 2016/2017 Champions League and drew 3-3 with Spains 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.