Even members of the Democratic Party, who Kyenge now represents in the European Parliament, approved a defamation case against Calderoli but without the charge of instigation to racial hatred.
Kyenge said she feels betrayed and is unsure whether she feels like staying with the party.
"What is striking is that this message comes at a delicate moment for Europe as it grapples with the rise of racism against immigrants," Kyenge was quoted in Il Fatto Quotidiano as saying.
Calderoli sparked outrage in July 2013 over the slur made at a rally in the northern city of Treviglio.
He said: “When I see Kyenge I can't help but think of an orangutan.”
He refused a call by then premier Enrico Letta to step down and has remained the deputy speaker of the Senate ever since.
He did apologise for the offense at the time, saying he had done “something stupid”. In his defense, he described himself as a “misunderstood animal lover” rather than a racist, and argued that the remark was made in jest
“I'd already forgiven Calderoli, it's no longer a personal issue," added Kyenge.
"Now it's a question of principle because the message that's coming out of the institutions to our children and young people is devastating."
Kyenge lost her ministerial position when Matteo Renzi became premier in February 2014.
The Senate's decision came despite Calderoli being known for his racist remarks.
After the football World Cup final in 2006, he said Italy had defeated France because the French national team was full of "negroes, Muslims and communists."
As integration minister, she was repeatedly subjected to racist attacks, some of which she is still pursuing through the Italian courts. One Northern League politician was earlier this year fined €150,000 for posting a photograph of Kyenge with an orangutan's face on Facebook.