Tottenham took the lead through a Harry Kane penalty after Clattenburg awarded a controversial spot kick in the 52nd minute, the referee deeming Raheem Sterling, who had turned his back to play, to have handled a Danny Rose cross.
Pellegrini subsequently accused Clattenburg of wanting to award the penalty and gave a scathing assessment of the same referee's performance in the reverse fixture last September.
"It was a penalty that referee Mark Clattenburg wanted to signal for and he gave the signal," Pellegrini said in a post-match interview.
"It was absolutely the wrong decision. It hit the back of Sterling, then his elbow. Sterling was not even seeing the ball.
"It was the same referee in the first game (at White Hart Lane) where there were two clear offside goals and we lost 4-1.
"For me, I don't think it is a good decision to have had the same referee."
The result marked the first time City have registered back-to-back home defeats in the league this season but captain Vincent Kompany said the team should not abandon hope of winning the title.
"We probably could have played a little bit better. Until the penalty, the game plan was okay and we were defending well," the Belgian centre-back said.
"But we would be stupid to forget our history and how we react in those moments."
(Reporting by Simon Jennings in Bengaluru; Editing by John O'Brien)
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