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It was a tighter margin than the first reading in August and was just as emotionally-charged.
Following the vote, Minister of Justice Andrew Little said that the bill was in good shape and he was optimistic about the committee stage next week.
"I was pleased with any number over 80 - so we got over that and we're there," he said.
"There could still be a further loss, we'll see how the committee stage goes."
In its first reading in August, the bill passed with 94 votes in favour, to 23 against.
After receiving 25,000 submissions changes were made to the bill, including safeguards to deal with sex selection, late-term abortions and to remove some of the barriers for women who require abortions.
After 20 weeks women now require not one, but two clinicians, to sign off on the procedure
National MP Agnes Loheni is staunchly against the bill and was quick to point out 91.6 percent of the submissions opposed the bill.
She said she was not scaremongering because there was plenty to be alarmed about, and diminishing the life of an unborn baby to the point they were no longer called babies meant humanity had been lost.
"Late-term surgical abortions are nothing short of barbaric,'' she said.
"There is nothing kind in it - a truly progressive society protects the rights of all its members down to the smallest and most vulnerable, the unborn child."
There was huge applause from the public gallery following her speech - prompting Speaker Trevor Mallard to threaten removal if it happened again.
Senior National MP Amy Adams supports the bill and has been working with Little to convince her side of the House to vote in favour.
Adams said she was disappointed that so few opponents had taken the time to understand the current realities of abortion care in New Zealand.
"Women are not fickle, inconsistent, hair-brained people who suddenly wake up one morning and decide they no longer want to be pregnant,'' she said.
"When abortions are sought post-20 weeks, it's very rare and because of the most tragic situations, and it is heartbreaking for everyone involved - it is offensive to suggest otherwise."
Labour's Greg O'Connor voted in favour of the bill at the first reading so it could go through the Select Committee process.
He hoped that would make the bill more palatable - but it did not.
O'Connor has an intellectually disabled 27-year-old son and said he knew the pressure that put on parents.
"What this post-20 weeks legislation will mean is that parents who do find out they have a child who may not be normal, who may be a child who isn't what they hoped the child might be, all of a sudden a whole new set of pressures are going to go on as a result of this legislation,'' he said.
National Party's Nikki Kaye said the country was the first to give women the vote, but was behind the times in its abortion laws.
"It's very simple, in fact it's so simple that we are one of the most archaic countries in the world," she said.
"Even Catholic Ireland has more liberal abortion laws than New Zealand."
The bill now heads to the committee stage where further changes can be made by MPs.
One of those changes that will be voted on is whether to have a referendum if the legislation passes - an amendment New Zealand First is pushing.
The election on 19 September will already include a referendum on both euthanasia and cannabis legalisation - shifting the more difficult conscience decisions away from Parliament and into the voting booth for the public to decide.