But the government agreed to Labour proposals for 13 new conditions to be met before shale gas extraction can take place.
During a Commons debate, ministers also pledged an "outright ban" on fracking in national parks.
Earlier, a committee of MPs called for a moratorium on the practice on the grounds that it could derail efforts to tackle climate change.
The Environmental Audit Committee also warned that there were "huge uncertainties" about the environmental impact of fracking.
Protests took place in Westminster as MPs gathered for a final Commons debate on fracking legislation in the government's Infrastructure Bill.
In the Commons, committee chair Joan Walley backed an amendment tabled by a cross-party group of MPs calling for fracking to be suspended for up to 30 months while an assessment is carried out.
Q&A: What is fracking?
But the measure did not attract front-bench support and was defeated by 308 votes to 52.
A Labour amendment was added to the bill, to loud cheers from opposition benches, which would impose 13 tests to be met before fracking.
These include the completion of an environmental assessment and the need to consult residents on an individual basis.
A ban on drilling in national parks was another of the suggestions in the Environmental Audit Committee's report.
After Labour and other MPs tabled amendments to allow the change to be made, Energy Minister Amber Rudd told the House that the government would remove the provision that shale gas exploration would be allowed in such areas in "exceptional circumstances".
She later said there would be an outright ban in "national parks, sites of special interest and areas of national beauty".

Raymond Dempster raped a 42-year-old woman in her home in Glasgow's east end and days later attacked a 19-year-old student in the city's west end.
Dempster, who has 110 previous convictions, had denied the charges.
At the High Court of Glasgow, Judge Norman Ritchie QC deferred sentence for background reports.
The court heard how the 38-year-old raped the first victim in her home on 20 June, three days after his release from prison.
The victim has since died, and her police statement was read out as evidence in court.
She told how she was locked out of her home in her nightclothes. When Dempster came along at first she thought he was a Good Samaritan.
She had said: "He told me once we were inside 'you've got a nice wee flat here'."
He then grabbed her by the arms and pushed her into the bedroom, removing her clothing and raping her.
The court heard that Dempster bit his victim and punched her on the face during her ordeal.
Dempster's other victim was walking home alone along Kelvin Walkway in the early hours of the morning on 23 June.
He followed her, then grabbed her, forced her to the ground and put his hand over her mouth.
The woman fought back kicking Dempster in the face, and he ran off to the hostel he was living in.
She said: " I believe his intention was to rape me."
Police found CCTV footage which showed Dempster in the vicinity of the attack and his victim identified him.
The prosecutor said that Dempster was jailed for five years in 2003 for rape and has breached the condition of the sex offenders' register five times.
His 110 previous convictions also included dishonesty and violence.
Judge Norman Ritchie QC said: "A man with his record is simply shown the door and then within a handful of days has attacked two women."
He told Dempster he would be considering whether to make an order for lifelong restriction.
MPs have overwhelmingly rejected a bid to suspend fracking for shale gas.
[NEXT_CONCEPT]
A convicted rapist has been found guilty of raping a woman and attacking another just days after being released from prison in June last year.