Lyon were in search of a third consecutive title, while the Germans were making their debut in the European club championship final at Stamford Bridge in London.
The French side had the better of the final but could find no way through and with 17 minutes remaining, after Laura Georges handled the ball, Martina Muller converted from the penalty spot.
Muller’s goal ensured Wolfsburg would be the first team to defeat the French champions over 90 minutes for 120 games.
Wolfsburg won the Frauen Bundesliga and German Cup in the past fortnight and their win at Stamford Bridge marks an historic treble for the club which before this year had never won a major trophy.
Ahead of the trophy hunt New Zealand defender Smith said the side would be seeking the treble, but expected it to be a difficult task.
The UEFA Champions League final on Saturday, 25 May will be an all German affair with Borussia Dortmund taking on Bayern Munich. This will be the first time two German side’s will hold the men’s and women’s titles at the same time.