environment secretary Owen Paterson and the Welsh secretary David Jones, defied appeals to vote in favour of the new bill as they believe it would impinge upon religious freedoms.
Others, such as the government's attorney general Dominic Grieve abstained, with some MPs deliberately voting in both lobbies to express how torn they were.
A small number of Labour and Liberal Democrats also chose to vote against the bill.
The Roman Catholic church said it would use the strong objections to the bill voiced by MPs across the House to maintain its campaign against same-sex marriage.
The Church of England, the country's official faith, is barred from performing such ceremonies. There is a provision in the bill to ensure that the Church, which opposes gay marriage, is protected from legal claims that as the official state religion it must marry anyone who requests it.
The provision says that all religious organizations can decide for themselves if they want to "opt in" to holding gay weddings.
"The Catholic Church continues to support marriage understood by society for centuries as the significant and unique lifelong commitment between a man and a woman for their mutual well-being and open to the procreation and education of children. Marriage is rooted in the complementarity of man and woman," said the Most Reverend Peter Smith, Archbishop of Southwark.
This week's vote comes nearly half a century after homosexuality was legalised in Britain and nearly nine years after the country introduced the Civil Partnership Act granting same-sex couples the same rights as those in civil marriages.
The bill's provisions apply only to England and Wales. Scotland is considering introduction of a similar bill, but there are no such plans in Northern Ireland.