Midfielder Thiago's replacement Renato Sanches made the most of his rare start in their 2-0 win at Benfica on Wednesday, scoring one goal and helping set up the other.
"All players who played in Lisbon are fit. Thiago will also complete our final training," Kovac said.
Bayern are still without injured Corentin Tolisso, Kingsley Coman and Rafinha.
Kovac said Sanches' performance in Portugal will earn him more playing time in that midfield role.
"Renato did it really well against Benfica. He confirmed our trust in him and he will play regularly in the coming weeks," Kovac said.
Bayern have won all three of their league games to top the table on maximum nine points, two ahead of Borussia Dortmund, and Thiago's return could not have come at a worse time for troubled Schalke.
The Royal Blues, runners-up last season, have lost all three games so far and sit at the foot of the table along with Bayer Leverkusen.
"At Schalke we want to pick up where we left off last week against Leverkusen," Kovac said. "I expect an aggressive and intense game.
"Their fans will push them. If we reach our limit, and we have to do it, then we will win the game."
(Reporting by Karolos Grohmann; Editing by Toby Davis)
