The decisions makes her the latest in a series of high-profile figures to leave the State broadcaster in recent months.
Berlinguer, the daughter of late Italian Communist Party leader Enrico Berlinguer, thanked Rai for having let her work for the network in total autonomy for 34 years.
She is reportedly set to join the Mediaset private network founded by late, ex-prime minister Silvio Berlusconi.
Rai3 also recently lost the two popular left-leaning chat show hosts, Fabio Fazio and Lucia Annunziata, a former Rai chair.
Fazio, whose show was not renewed is moving to Discovery Channel.
He said in mid-May the failure of Rai to renew the contract for his historic talk show was a sign of the “boundless greed” of the new government in the alleged purge.
In his weekly column for Oggi, Fazio said the right felt “legitimised” by its thumping September general election win.
“[They believe they can] behave like the owner of the public sphere with little regard for the public weal and with a boundless greed,” he wrote.
Former Rai president and veteran journalist Annunziata quit Rai complaining about government meddling.
Appointments to the State broadcaster have always been heavily influenced by the government of the day, with the exception of Rai 3 which had retained its identity as a left-leaning channel.
ANSA