"It's all about the frustration of the player," Koeman was quoted as saying by the club's website (www.saintsfc.co.uk).
"He was not playing well, he was not scoring and the team was not winning, but you have to control yourself always.
"We have to accept it and we will play another (number) nine next week."
Koeman will have strikers Shane Long and Sadio Mane available next weekend, but Jay Rodriguez is facing ankle surgery and a lengthy spell on the sidelines.
Pelle's absence is a blow for the manager ahead of the trip to face a City side that will look to get their season back on track after being defeated 4-1 by Liverpool on Saturday and knocked off their perch at the top of the table.
Of equal concern to the Southampton manager was his side's limp display against Stoke, that saw them drop a place to eighth in the table on 20 points, ahead of Liverpool and behind Everton on goal difference.
"It was not the level what we expect and what we can bring," the manager said.
"My team was different than normal. I felt already before the game a different belief, different atmosphere."
(Reporting by Simon Jennings in Bengaluru; editing by Sudipto Ganguly)
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