The victory was enough for the Royal Blues to secure their place in the knockout stage with one group game remaining, but Magath was quick to turn his attention to the Bundesliga, where Schalke are still struggling to live up to expectations.
"I hope that we can carry the momentum from this 3-0 win over Lyon into our coming games," said Magath. "Unlike in the Champions League, we are still lagging behind in the Bundesliga."
Schalke are 15th in the German top flight after a run of three wins in 13 - the same number of victories they have claimed in their five Champions League Group B outings.
Yet Magath has reasons to be optimistic after what he saw at the Arena AufSchalke last night.
"To have qualified for the knockout stages of the competition with one game still to go in the group stage is very satisfying," he added. "I think that the first half was the best that we have played so far this season. My team has continued its positive development."
Klaas-Jan Huntelaar was once again Schalke's hero with two goals, taking his tally to nine since arriving at the club in August.
"I am delighted to be able to help my team," Huntelaar said. "Now we have got to concentrate on our next Bundesliga game against Kaiserslautern and play equally well there."