Champions City could have closed the deficit to two points with the west London side playing Tottenham Hotspur in the Capital One (League) Cup final.
Instead City remain five points adrift having played one game more after Jordan Henderson and the outstanding Philippe Coutinho scored "beautiful" goals either side of Edin Dzeko's equaliser.
"Of course it is difficult to reach the top of table if you lose three points," Pellegrini told Sky Sports.
"It is three points less with one game less. It was a close game but Liverpool won because they scored two beautiful goals.
"But we must keep going and try to return to our normal performance and see where it takes us."
City were out of sorts at Anfield and looked flustered in the face of Liverpool's high-octane pressing which disrupted their trademark slick passing.
After four successive games without victory in January and February, City appeared to have reignited their title challenge with victories against Stoke City and Newcastle United, with an aggregate score of 9-1.
After defeat, however, Pellegrini said there was still much for his expensively-assembled squad to improve on.
"There is much we must analyse to improve. I'm concerned that we are losing the ball too much, pressure is a factor," the Chilean added.
"In the first half we lost too many balls, especially in the first 15 minutes. After that we equalised and then hit the post through Aguero.
"But in the second half we didn't arrive in their box so we tried to change our style of play."
City have 11 league games remaining to catch Chelsea, starting with the visit of bottom-of-the-table Leicester City on Wednesday.
(Reporting By Tom Hayward; editing by Toby Davis)
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