Lyon will play French rivals Paris Saint-Germain in the UEFA Women’s Champions League semi-final on Wednesday 26 August.
Katoto scored one and made another as PSG eliminated Arsenal
PSG took a 15th-minute lead when Marie-Antoinette Katoto was allowed to meet a corner on the volley to hook it home.
Kim Little missed a great chance to level from Noelle Maritz’s pass soon after but in the last 10 minutes of the half, played in Beth Mead who fired into the far corner.
Signe Bruun marked her return from long-term injury by coming off the bench and restoring the lead when meeting Katoto’s ball across the six-yard area 13 minutes from time.
Majri set-piece seals Lyon’s progress
Holders Lyon head a narrow half-time lead over Bayern Munich, Nikita Parris with a brave headed opening goal.
Amel Majri doubled the lead from a free kick just before the hour mark but Carolin Simon replied to get Bayern back in the tie with another set piece five minutes later.
The semi-finals are live on BT Sport 1 at 7pm (UK time) next Tuesday and Wednesday.