The Government motion of confidence in Simon Harris was passed after 94 TDs voted in favour and 65 against.
Before the vote, Aontú leader Peadar Tóibín defended tabling the original motion of no-confidence in Mr Harris.
"If the death of a child, if the continuous painful suffering of a child, of hundreds of children, if the disablement of hundreds of children is not reason enough for a motion of confidence, what the hell is?" Mr Tóibín said.
Sinn Féin leader Mary Lou McDonald said that she has no confidence in the Tánaiste and neither do the families "let down" by him.
"God hurry the day" when he will be removed from power, she told the Dáil, and claimed the "making and break of promises has come to define" Mr Harris, leading to "deep hurt, pain and anger".
Labour leader Ivana Bacik said her party could not vote for the confidence motion, which she said derived from a broken promise.
This was just one in a litany of broken promises on the delivery of the National Children's Hospital, childcare and people awaiting a home, she added.
Mr Harris said that he has never claimed to be infallible and does not get everything right, but he always acted in good faith.
He told the Dáil that he was very conscious of the death of Harvey Morrison - a boy who was subject to delays in accessing urgent scoliosis surgery - and he had expressed this to his parents.
Mr Harris also said that the Government was working on the structure of an inquiry into scoliosis and spina bifida services, and he would have further meetings with the nine-year-old's parents.
Taoiseach Micheál Martin described the Tánaiste as a diligent and dedicated minister who was helping to lead the country through perilous times.
Earlier, Mr Tóibín accused the Government of being "incredibly cynical" by bringing forward the motion of confidence in Mr Harris to this week, pre-empting his party's plan to table a no-confidence motion next week.
Speaking on RTÉ's Morning Ireland, Mr Tóibín said that Aontú was not playing politics by putting down such a motion in the last week of the presidential campaign.
His party had said during the summer that it would take such action at the first opportunity, he added.
Mr Tóibín said that Aontú "may" put down a no-confidence motion in the Government next week.
He accused Mr Harris of failing significantly to deliver on a promise he made, as minister for health, that children would not wait longer than four months for a scoliosis operation.
He spoke too about what he termed a "crisis" in Children's Health Ireland (CHI).
We need your consent to load this rte-player contentWe use rte-player to manage extra content that can set cookies on your device and collect data about your activity. Please review their details and accept them to load the content.Manage Preferences
The Government is working with advocacy groups to agree the structure of the inquiry into spina bifida and scoliosis services at CHI.
Minister for Health Jennifer Carroll MacNeill met families and a follow up meeting is being arranged to discuss options.
