Mr Javid, who stripped the Islamic State bride of her British citizenship, said any blame for the infant’s death lay fully with jihadists.
He told the House of Commons: “The death of any British child, even those children born to a foreign terrorist fighter, of course is a tragedy - but the only person responsible for the death of that child is the foreign terrorist fighter.”
The case of Ms Begum, born in Bethnal Green but who travelled to Syria to be with Isis as a “jihadi bride” aged 15, was raised in the Commons during an urgent question on Monday.
Shadow home secretary Diane Abbott had suggested Mr Javid’s act was responsible for Ms Begum’s infant son Jarrah dying from pneumonia in a Syrian refugee camp on Friday.
Ms Abbott questioned if stripping Ms Begum of her nationality “made it impossible for her to fulfil her duties as a mother and bring her baby home to a safe place?”
The MP for Hackney North and Stoke Newington had asked Mr Javid: “Nobody on this side of the House condones what Shamima Begum did, the choices she made, the things she said... If it was his 19-year-old daughter, however badly she had behaved, however reprehensible or near-criminal her choices would he want her to bury three babies in the course of a year?”
The exchange came as Tasnime Akunjee, a lawyer for Ms Begum, called on the Home Office to reinstate her British citizenship as “an act of mercy”.
The 19-year-old, who fled the UK for Syria four years ago, has given interviews from the camp saying she wished to return to the UK for the baby’s safety after her two older children died.
The letter to the Home Office, also posted on Twitter, said: “We write specifically on behalf of Mrs Begum, Shamima Begum’s mother, to ask you to reconsider your previous decision dated February 19 2019 to deprive her daughter Begum of her British citizenship ...
“Ms Begum requests this reconsideration, as an act of mercy, on the basis of the following new information, namely the death of her newborn son.”
It adds: “It is extremely unlikely that Shamima will be in a fit state to make any rational decisions.
“The family have still not been able to contact her directly and their request for any help from the British government to contact Shamima and her baby was refused in writing by the Home Office on March 5.”
In the wake of the baby’s death, Foreign Secretary Jeremy Hunt said officials are working on how to rescue British children born to Islamic State runaways.
The Foreign Secretary’s defence came after it was reported two further women married into the terror group have been stripped of their UK citizenship while being held in detention camps with their children.
The Government had suggested Ms Begum could apply for a Bangladeshi passport but this was refused.
Her family claim UK officials had not consulted Bangladesh before making their decision.
Mr Akunjee added: “You will appreciate there are immediate fears for Shamima’s health and safety, and the matter is urgent.”