Benfica were disappointing throughout but Lyon's late equaliser in the 2-2 draw against Hapoel Tel Aviv in the night's other Group B game meant the Portuguese champions finished third and grabbed a Europa League place.
"I did not want to know what was going on in the other game, but we finished third thanks to the Lyon draw. That's football, and we ending up benefiting," Benfica coach Jorge Jesus said.
The German team scored with their first real chance of the game when Ivan Rakitic's cross was chested down by Raul for his fellow Spaniard Jurado to fire in on 19 minutes, with a static Benfica defence caught ball-watching.
"The priority was to win, go through to the Europa League with nine points and not think about third parties. We didn't play well in the first half, we were not dynamic and the players were too rooted to their positions," Jesus added.
Schalke doubled their lead in the 81st minute when Howedes beat an offside trap after a corner to finish coolly from near the penalty spot before Luisao headed in a consolation goal for the hosts.
FANS BOO
Lacking aggression going forward, Benfica's sole clear chance in the first half was a fierce long-distance effort by midfielder Carlos Martins that went just wide.
The Lisbon club have failed to repeat last season's impressive performances and the fans, already unhappy that the side are eight points adrift of Porto in the domestic league, made their point by booing the team during parts of the game.
"Unfortunately things have not been going like we want. We are anxious to change matters quickly and sometimes that is hurting us. We have to keep our feet on the ground, we still have the Europa League," defender David Luiz said.
Even without putting their foot on the gas, Schalke looked dangerous, with Rakitic and Jurado lively on the flanks and Klaas-Jan Huntelaar combining well with Raul to make the Portuguese side look vulnerable.
Benfica introduced Argentine duo Pablo Aimar and Nicolas Gaitan at half-time but Schalke continued to control the match and came close in the 54th minute when Peer Kluge beat Fabio Coentrao in the box only to send his scuffed effort wide.
The Portuguese team slowly started to threaten and created two chances in quick succession around the 65th minute, with Javi Garcia sending a first-time shot wide and Oscar Cardozo forcing Manuel Neuer to block a powerful drive moments later.
