Mourinho was furious with the effort from his players after the game, branding their performance "too soft" as late goals from Yoan Gouffran and Loic Remy saw the hosts triumph.
The Portuguese has promised to make changes for the visit of Schalke as Chelsea go in search of their 100th win in Uefa competition."I will make changes. Not 11 changes because that would be too much, but changes for sure," Mourinho told the club's official website.
"I don't know my best team because we have this kind of performance [against Newcastle]."
Chelsea top Group E with six points from three matches, having bounced back well from a shock 2-1 home defeat to FC Basel in September.
That result represented Chelsea's first loss in 30 home group-stage fixtures, but the club have since recorded two comfortable victories on the road, including a 3-0 win at Schalke last month.
Fernando Torres scored twice in Gelsenkirchen before Eden Hazard added polish to the scoreline with a late goal.
Marco van Ginkel (knee) is the only injury absentee for Chelsea, who sit second in the Premier League - five points behind table-toppers Arsenal.
Schalke enter the match on the back of a 2-0 win at Hertha Berlin on Saturday, a result that lifted them to sixth in the Bundesliga table.
Adam Szalai and young star Julian Draxler scored the goals for Schalke, who are now unbeaten in their last seven away matches, with six of those finishing in wins.
Schalke enjoyed success on their previous visit to the English capital, defeating Arsenal 2-0 in October last year.
They sit second in Group E, behind Chelsea on goal difference alone, and will be eager to atone for events in the reverse fixture, which saw the club suffer their worst home loss in the Champions League.
Schalke fans are excited about the development of Max Meyer, who became the youngest player in Bundesliga history to score in three successive games last month aged 18 years and 38 days.
Klaas-Jan Huntelaar will be missing, however, after suffering a recurrence of his knee injury in training last month.
The Netherlands forward scored four goals in last season's Champions League, but will not play again this year.
Jefferson Farfan (groin), Marco Hoger (knee) and Chinedu Obasi (tibia) will also miss the trip to Chelsea, while Greek defender Kyriakos Papadopoulos (knee) is a doubt.
Papadopoulos played 90 minutes for Schalke's reserves on Saturday but the 21-year-old has not played a first-team game this season.