In the deepest split yet between the coalition parties, Liberal Democrats combined with Labour and smaller parties to delay the implementation of the boundary review - thought to be worth about 20 extra seats in the Commons to the Tories - until 2018.
For the first time since the coalition's formation in 2010, Prime Minister David Cameron agreed to set aside the convention of collective responsibility and allow Liberal Democrat ministers to vote against the Electoral Registration and Administration Bill.
Mr Clegg initially supported the changes as part of a package of constitutional reforms, but announced last summer that his party would try to delay the review after the Tories forced the abandonment of plans to reform the House of Lords.
A senior Liberal Democrat source said the vote, which saw the Conservatives defeated by a margin of 292 to 334, would have no impact on the future of the coalition.
"The coalition is fine," said the source.
"Both sides of the coalition have known what the position is for months now. There are 101 other things the Government is doing and we will get on with those.
"This vote now draws a line under this issue."
But there was fury on the Conservative benches at the Lib Dem decision to vote against legislation to equalise the size of Westminster constituencies and reduce the number of MPs from 650 to 600, which Mr Clegg had previously championed as a matter of fairness.
Tory Penny Mordaunt said the Lib Dems were motivated by "spite, pettiness and self-interest" and were making "flirtatious glances" to Labour as potential coalition partners following the 2015 poll.
"The Liberals have exchanged their legendary sandals for flip-flops in the hope that it will enable them to keep their options open," she said.
Amid scenes of rancour on the Tory benches directed at their Lib Dem coalition partners, Commons Leader Andrew Lansley appealed in vain for MPs to overturn a House of Lords amendment postponing the boundary changes, which he denounced as "an abuse of parliamentary process".
But all 57 Liberal Democrat MPs voted in favour of the amendment, with four Tory rebels. And there was no sign of smaller parties rowing in to support the Conservatives, with only one - Naomi Long of the Alliance - joining them in the Yes lobby.
Mr Lansley said the delay will mean the 2015 election being fought on boundaries 15 years out of date, with "some votes counting more than others" due to disparities which have resulted in East Ham having an electorate of 92,000 while Wirral West had just 55,000.
Reform would have supported "the principle of greater equality in the value of each vote" and cut £13.5 million a year from the cost of democracy, said Mr Lansley.
But shadow justice secretary Sadiq Khan said the ditching of the proposals meant that "selfish and partisan" changes had been "stopped in their tracks by peers and MPs from all sides".
Mr Khan said: "David Cameron should try to win elections fair and square and not by moving the goalposts.
"It would have been an insult to democracy to reduce the number of elected MPs by 50, while over 100 new unelected members of the House of Lords have been created since the last election with another 50 reportedly due very soon."
Following the vote, Mr Lansley told the BBC: "I think the public are going to, rightly, find it difficult to understand how two years ago Parliament could vote for the number of MPs to be reduced, for the value of votes in each constituency so far as possible to be equalised by making constituencies closer to an equal number of electors, and two years later you get a different result.
"Why do you get a different result? Because the Liberal Democrats in the first instance voted for the reform and today voted for that reform not to take place before the general election."
Mr Clegg was wrong to link the boundary review with reform of the Lords, said Mr Lansley.
"From our point of view - and the Deputy Prime Minister agreed - there was no link between progress on House of Lords reform and constituency boundaries," said the Leader of the Commons.
"In the Coalition Agreement, we linked together the referendum on alternative votes with boundaries."
Asked if tonight's vote would make it more difficult for the Tories to win an outright majority at the next election, Mr Lansley replied: "It may do. We will fight the election on whatever the constituency boundaries are at that time. We will fight the election to win it."
Mr Lansley brushed aside suggestions the coalition might be fatally wounded, pointing out that Mr Cameron and Mr Clegg had jointly launched a Mid-Term Review setting out the Government's plans for the remainder of the parliament, at a time when the Lib Dems had already made clear they intended to block the boundary review.
"You come together in a coalition agreement, and if you live by that agreement together, then actually you can live with some of the disagreements that occur from time to time," he said.
The Scottish National Party welcomed the Tory defeat, and said earlier speculation that it was considering voting with the Conservatives was "ludicrous".
SNP MP Pete Wishart said: "I welcome the vote. However, accusations that the SNP were working for a deal with the Tories to hinder Scottish Labour are ludicrous.
"We had no intention of supporting the Conservatives in any vote on the boundaries plan and no discussions took place.
"The only other party working for the Tories is Labour in the No campaign, working to keep Scotland governed by Conservatives at Westminster."