The Independent Group MP said her family were "brimming with happiness" at the new arrival.
She praised the "fantastic team" at Liverpool Women's hospital on Twitter for looking after them.
She tweeted: "Our baby boy arrived yesterday – Alistair, Amelie and I are brimming with happiness.
"A massive thank you to the fantastic team @LiverpoolWomens for looking after us both with so much care."
It's her second child with music producer Alistair Goldsmith.
Ms Berger was heavily pregnant when she left Labour two weeks ago over Jeremy Corbyn's failure to get a grip on anti-Jew hate in the party.
Deputy Leader Tom Watson said it was the "worst day of shame in the party's 120-year history" that she was hounded out.
She took part in several media interview and press conferences too afterwards – her last one was just last week.
But today Mr Corbyn delivered his congratulations to her in the House of Commons.
He said during Prime Minister's Questions: "Can we congratulate the member for Liverpool Wavertree for giving birth to a son this morning."
While heavily pregnant she also faced efforts to try and kick her out of her local Labour party too – until those who tabled motions of no confidence against her were forced to withdraw them.
Last weekend she said she was forced to report threats against her unborn child to the police.
One former Labour member tweeted her to say: "Lets all pray the same fate awaits @LucianaBerger's baby that she wishes for all Palestinian babies."
She told The Times: "I can't run quickly at the moment, I've got every measure I possibly can to make sure my home and office are safe."
Last year the abuse was so serious she had to have a police escort to accompany her across the party's conference in Liverpool.
Prime Minister Theresa May also wished her well this afternoon during Prime Minister's Questions.
Friends have congratulated her on the bundle of joy, whose name has yet to be revealed.
Her colleagues at the Independent Group tweeted a picture of a baby-grow they had bought her which read: "#ChangePolitics & nappies" – in a reference to their new party.
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