The Argentine club were knocked out of South America's premier club competition on Thursday following a 3-1 home defeat to Atletico Nacional of Colombia in their final group fixture.
The result capped a run of four matches without a win in all competitions, which included a 1-0 derby defeat at home to Rosario Central on Sunday.
Berti, who replaced Gerardo Martino, who took over at Barcelona, in July, leaves Newell's 14th in the Argentine Primera Division's final championship, with 14 points from 12 games.
"Today my link with Newell's ends," he told a press conference at the club's Estadio Marcelo Bielsa on Friday.
"Given that this run of results wasn't good, I've decided to step aside."
Newell's had reached Argentine top-flight final under Martino in 2013 and made the last four of the Copa Libertadores in the same year.
Ricardo Lunari will take control of the team for Sunday's clash with Godoy Cruz.
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