The S04 boss feels the Switzerland side are expected to win against his men after overcoming Chelsea on the first matchday in London
The Swiss outfit stunned the Blues 2-1 at Stamford Bridge on matchday 1 and the 42-year-old believes his side will now approach the clash at St Jakob Park as underdogs.
"Basel have beaten Chelsea at home, so they are the favourites," he told a press conference.
"However, we travelled to Switzerland in order to gain something. Basel have a lot of variety in their game, they like to change their tactics during the match. Also, they're very stable at the back.
"We are prepared very well for our opponents. Especially their win at Chelsea drew a lot of attention. They have many good offensive players, so we'll have to play well defensively."
Julian Draxler missed the weekend's 3-3 thriller with Hoffenheim with a knee injury, but Keller went on to confirm that the young Germany international should be fit to feature.
"I'm certain that Draxler will be able to make an appearance after his knee injury," he added.
Schalke and Basel kick off at 20:45CET on Tuesday.