Chris Turner got the goal for the home side, who dominated the contest for large spells, just after half an hour into the match, the first leg of the second qualifying round.
The Estonians could have secured an altogether different result, though, had Valeri Minkenen tucked away a penalty just moments earlier - but Alan Mannus made a crucial save to a tame shot.
Rovers now travel to Tallinn with the advantage for the second leg.
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