Alex Popp hit back for the German side with a smart header, but Lyon were too strong, too savvy and too collected – and Iceland midfielder Gunnarsdottir rubber-stamped the win with a late third.
Lyon had to battle hard but fully merited their record seventh Champions League success, in their ninth final in 11 years.
The French giants have not tasted defeat in competitive action since a 1-0 loss to Paris St Germain in the French cup final back on May 31, 2018.
England's Lucy Bronze finished her Lyon career in style, bowing out with a hat-trick of European titles.
The 28-year-old has yet to reveal her next destination, but sealed the ideal exit as Lyon prevailed in San Sebastian.
Two-time winners Wolfsburg fell to familiar foes Lyon again, unable to dislodge the French side in their fifth final.
Gunnarsdottir only joined Lyon in July – making the switch from Wolfsburg. The 28-year-old turned out for the Germans earlier in this season's competition, but the coronavirus-delayed campaign meant she faced her old club in the final.
Lyon dominated from the off, Europe's outstanding talents again showing all the poise and polish required for another triumph.
Le Sommer put the defending champions ahead, sweeping home at the second attempt having had her first effort parried by Friederike Abt.
The lively Delphine Cascarino had created the opportunity, charging down the right flank and laying on a smart cutback across the area.
Wolfsburg shook off the setback and settled into the contest, but crucially were unable to carve out any genuine chances.
And Lyon punished the Germans just ahead of the break, thanks to Kumagai's high-quality strike.
The Japan midfielder drilled home from the edge of the area with a fine technical finish, to leave the French side in total control at the break.
Lyon eased into the second half and appeared entirely comfortable, only for Wolfsburg to snatch a lifeline just ahead of the hour.
Ewa Pajor delivered a smart cross in latching onto Lyon keeper Sarah Bouhaddi's fumble, and Popp reacted adroitly with the snap-header finish.
Wolfsburg's bid for an equaliser was ultimately ended by Gunnarsdottir's scrambled finish, following Le Sommer's driven shot as Lyon emerged victorious once again.