With the match inching towards a penalty shootout, Sarri was set to turn to Willy Caballero, who had featured for City from 2014-17.
But Kepa waved his manager off, electing to remain on the pitch before City edged Chelsea 4-3 on penalty kicks.
And now, Kepa has been excluded from the club's first match since the incident with Sarri saying it was his decision to start Caballero in his stead against Spurs.
"It's a choice. It's a message for my group. We are a group - not 25 players. It is my choice," Sarri said on BT Sport.
Kepa had started all 26 of Chelsea's Premier League matches this season as well as four Carabao Cup games and six Europa League ties.
In the aftermath of Sunday's incident, Kepa came out to say it was never his intention to go against Sarri while adding that he understood it wasn't the best image to portray.
Sarri, meanwhile, clarified the incident was a "misunderstanding" while saying that he hoped to move on quickly.
Still, the goalkeeper was fined a week's wages for the ordeal with the money going to charity.
Sarri's choice was backed by former Chelsea midfielder Joe Cole, who agreed with the decision to drop the goalkeeper.
"He has got it spot on, we were all talking earlier and he has absolutely done the right thing. He has asserted that he is the leader," Cole said on BT Sport.
"This is the message to the team. He will live or die by it tonight. The pressure is on Willy Caballero to perform.
"The message in the long term is this is my team and my group. No one is going to step out of line and I applaud him for it. It is a great decision."
While Caballero earned the nod against Tottenham, it remains to be seen if Kepa will earn a recall in time for Chelsea's next match, a visit to Fulham on Sunday.