Sunday trading hours will remain the same at present after MPs voted by 317 votes to 286, majority 31, to scrap the proposal from the Enterprise Bill.
Shadow business secretary Angela Eagle said the government should now abandon “tawdry attempts” to force the plans through parliament.
But communities minister Brandon Lewis accused the SNP of hypocrisy, as similar measures are already in place in Scotland.
“Majority in English and Welsh MPs for Sunday Trading,” he posted on Twitter. “SNP stop rest of country have freedom Scotland has.”
MPs were denied the opportunity to debate the 11th-hour compromise, after Speaker John Bercow declined to provide Commons time. Ministers then tried to win over sceptics by promising the pilot scheme will instead be tabled in the House of Lords if they reject the rebel amendment.
Meanwhile, the Business Department released the results of an official assessment of the potential impact of extended Sunday trading hours, which suggested liberalisation could benefit the UK economy by an estimated £1.5 billion or more over ten years.
Individual households could expect to benefit by the equivalent of £29 as retailers pass on savings generated by the ability to maximise the use of large stores, the department suggested.
Setting out details of the latest concession, Mr Lewis said the government was ready to ditch its plan to extend powers to set Sunday opening hours to councils nationwide on the first day of the new regime.
Instead, it will invite local authorities to apply for places on the year-long pilot scheme. Twelve locations, which are nominated locally and are “geographically, economically and demographically diverse” will be selected to take part in a study to determine the impact of liberalisation.
The prospect of a damaging Commons defeat was raised after the SNP said it would vote with Tory rebels to block the Sunday trading measure.
The move - after the nationalists had previously indicated they would abstain - infuriated ministers, with one Government source branding their action as “disappointing and hypocritical”.
Mr Cameron joined last-ditch efforts to stave off defeat by speaking personally to Tory MPs with concerns about the impact of longer Sunday opening hours on family life and the viability of smaller shops.
Addressing MPs after the defeat, Business Secretary Sajid Javid said he had “respect” for those who opposed Sunday Trading in principle.
“However, I am extremely disappointed by the childish and hypocritical actions of the SNP.”
Pressed on whether the government would now drop the plans altogether, Mr Javid stressed that the majority of English and Welsh MPs had supported the change.
“It was denied because of the SNP,” he added. “The only thing the SNP was interested in today was headlines.”