Jule Brand and captain Ada Hegerberg -- the competition's all-time leading scorer -- also found the net for the record eight-time champions.
The 18-year-old Yohannes spotted goalkeeper Carina Schlüter off her line in the 52nd minute. From near the center circle, Yohannes powered a right-footed shot over Schlüter's head and into the net.
Brand opened the scoring just before the half-hour mark in France. The German completed a fluent move by Lyonnes by tapping in a cross from Vicki Bècho.
Hegerberg headed in the second just seconds before halftime to improve her total tally to 67.
Lyonnes amassed 44 attempts on goal compared to six by the visitors from Austria. The French side's coach Jonatan Giráldez used an entirely different starting 11 than the one that beat defending champion Arsenal 2-1 in the first round a week ago.
St. Pölten lost 6-0 to Atleti at home last week.
In the new format, the 18-team league phase ends in December. Teams that finish first to fourth in the standings advance directly to the quarterfinals. Those ranked Nos. 5 to 12 go to a knockout playoff round. The bottom six teams are eliminated.
In Wednesday's other action, two-time champion Wolfsburg needed Janina Minge's penalty kick deep into stoppage time to win 2-1 over Vålerenga.
Lineth Beerensteyn capitalized on a defensive blunder, burst into the area and scored with a low shot past goalkeeper Tove Enblom to put Wolfsburg ahead 1-0 in the 57th minute.
Sara Hørte equalized just three minutes later with a header.
Wolfsburg routed Paris Saint-Germain 4-0 last week, when Vålerenga lost 1-0 at Manchester United.