In the first-ever debate resulting from an online petition, it lost a backbench business motion calling on it to cancel the pilot culling schemes and find other ways to defeat the disease, which cost the lives of 26,000 cattle last year.
The voting was 147 in favour of the motion and 28 against.
While very disappointed by the result, which is not binding on Government policy, Westcountry farmers are calling on Ministers to show fortitude and press ahead with the culls in West Somerset and around Tewkesbury in late spring next year.
"It would be a pretty sorry state of affairs if Government policy were dictated by internet campaigns run by pressure groups," said Ian Johnson, regional spokesman for the National Farmers' Union in the South West.
But the badger cull was ill-judged and deeply unpopular, said Green MP Caroline Lucas, as MPs from across the political divide called for the abandoning of the controversial policy.
Miss Lucas told MPs that shooting badgers would never achieve the Government's target of reducing bovine TB by 16%, and she accused Tory MPs who supported the ban of being emotional. She said any cull would only move the problem elsewhere, while one trial which destroyed 10,000 badgers had limited success.
The MP for Brighton Pavillion had tabled a motion calling on the Government to "stop the cull and implement a more sustainable and humane solution" of vaccinating against TB, and improved testing for the disease.
Twenty-nine other MPs from all three main parties signed the motion, including the Tory MPs Zac Goldsmith and Tracey Crouch, while more than 160,000 people put their names to an online petition.
The heated debate came after the Government announced on Tuesday it planned to delay the culling of badgers until next year as there were more of the animals than anticipated.
Speaking in the Commons, Miss Lucas said: "While Tuesday's announcement to suspend the cull is very welcome, it does not amount to a change in policy. Today's motion calls on the Government to stop its ill-judged, unscientific and deeply unpopular culling policy for good, not just for a few months. This motion is about an abandonment of a cull, not just a postponement. That's what the majority of the public wants and it is what the science demands. Public opinion overwhelmingly opposes a badger cull, including in those places where a pilot is due to take place.
"The scale of the problem is such that it is deeply irresponsible and unfair to gamble, as this Government is doing, with farmers' livelihoods and with the future of one of our best-loved wildlife species."
Miss Lucas said she understood the distress caused to farmers by bovine TB, but claimed culling actually increased the prevalence of the disease in badgers.
Earlier, Environment Secretary Owen Paterson said it was "completely essential" the Government continued with the cull.
He told MPs he had: "every intention that these culls go ahead. There will be time to prepare, there will be no hitches next year, we shall deliver this policy. It is completely essential that we go ahead with these culls and prove that they will work, so that we bear down on disease in wildlife and we bear down on disease in cattle."
Tiverton and Honiton Tory MP Neil Parish said: "We are taking out the cattle with TB but we are not taking out and controlling the badgers."
Conservative Mel Stride (Central Devon) said it was "simply impractical" at the moment to consider vaccination of badgers as a sensible way forward before achieving a reliable oral vaccine. There were not the resources to trap badgers individually and inject them.
And Tory Geoffrey Cox (Torridge and West Devon) said: "What we are doing here is not out of some bloodthirsty desire to kill, but is a serious reaction to a pressing problem, is sincerely intended, is meant to tackle the disease, a disease that so badly requires to be tackled for the sake of the country."
