Maurizio Sarri claimed Kepa Arrizabalaga seemingly refusing to be substituted during the EFL Cup final was a "misunderstanding".
Kepa twice required treatment during extra time at Wembley on Sunday, with Willy Caballero - Manchester City's shoot-out hero in the 2016 final - prepared to come on.
Sarri appeared to be furious as Kepa defied his order to come off, with Caballero left confused on the sidelines during a long delay.
After 120 goalless minutes, City went on to win 4-3 on penalties, Kepa saving from Leroy Sane but allowing a weak Sergio Aguero effort to creep beyond him, with Raheem Sterling converting the decisive kick.
Sarri, though, would not condemn Chelsea's record signing as he explained his view of the incident.
"In that situation there was a misunderstanding," Sarri said to Sky Sports. "I understood there was a problem and we needed a change.
"I realised the situation and the doctor arrived to the bench after four minutes. It was a big misunderstanding.
"I understood the goalkeeper has cramp. I thought he could not do penalties, but the problem was not that bad and he was able to do the penalties."
Sarri appeared to consider leaving the Wembley pitch during the bizarre incident before returning from the tunnel area.
"No no, I needed only to be calm and quiet," the Chelsea boss added, repeatedly opting not to refer to Kepa by name.
"As I said to the goalkeeper, I asked for a change for his physical problem and he said I haven't got a physical problem. So he was right I think.
"When the doctor arrived to the bench [he said] the goalkeeper had a little problem and I wanted Caballero ready. "I have to talk with him [Kepa] to clarify because now I understand very well the situation." Chelsea were demolished 6-0 at City in the Premier League two weeks ago but showed a vastly improved display after Sarri used Eden Hazard as a false nine, dropping Gonzalo Higuain to the bench.
"They played exactly how I asked them. Today I am proud of my players," Sarri continued. "You have to ask the club [about his future]. Here I am really very happy.
"In the last three matches we are improving, we have improved a lot. Today we showed to everyone we can become a very solid team.
"We conceded nothing to the opponents and against City it is not easy. So really very happy with my players and proud of my players.
