The bill, which passed 289 votes to 230, will change the law so that people who arrive in the UK illegally will be detained and then promptly removed, either to their home country or a safe third country such as Rwanda.
Critics of the bill have dismissed the proposed legislation as unworkable, while right-wing Tory MPs believe it does not go far enough.
Other Tories want greater protections for minors and victims of human trafficking.
Ministers have already given in to some demands to avoid potential revolts, with a series of government amendments approved in the Commons.
The government was unable to say whether the legislation complies with the European Convention on Human Rights.
Although the bill has cleared the Commons, it will face a stiff test in the Lords, where it will undergo further scrutiny.
Senior backbench Tories, including former prime minister Theresa May and ex-party leader Iain Duncan Smith, voiced concerns about the impact the government's flagship immigration reforms could have on modern slavery protections.
UK government unveils 'robust' bill to stop migrant Channel crossings — in pictures
Ms May warned that it would leave more people in slavery in the UK, calling it a “slap in the face” for anyone who cares about victims of human trafficking.
“Modern slavery is the greatest human rights issue of our time. The approach in this bill, I believe, will have several ramifications,” she told the Commons.
“I believe it will consign victims to remain in slavery.”
Mr Duncan Smith said: “We need to send the right signals about this and I think the problem with this bill right now is it's unnecessarily now targeting a group of people that are not the problem, themselves will suffer, and ironically we will fail as a government through the home affairs end of it because the police simply won't be able to get those prosecutions.”
Earlier, Home Secretary Suella Braverman failed to offer statistical evidence to back her claim that migrants crossing the English Channel are linked to “heightened levels of criminality”.
She said people arriving in the UK in small boats have values which are “at odds with our country” before MPs debated the bill.
Asked later whether she had figures to support the statement, she said it was based on information she had gathered from police.
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“I think that the people coming here illegally do possess values which are at odds with our country,” the Home Secretary said earlier.
At an event later in Westminster, she added: “Not in all cases, but it is becoming a notable feature of everyday crime-fighting in England and Wales.
“Many people are coming here illegally and they're getting very quickly involved in the drugs trade, in other forms of exploitation.”
Asked whether that claim was based on empirical evidence, she said: “I consider police chiefs experts in their field and authoritative sources of information.”
Labour condemned Ms Braverman's comments about migrants' values, with a spokesman calling it the “sort of invective” that signals that the policies being promoted “have failed”.
Campaigners accused her of fanning the flames of xenophobia and racism.
“Suella Braverman's dog-whistle remarks about the 'values' of migrants being 'at odds' with British 'norms' are appallingly divisive and shamelessly intended to stoke fear and hatred of people seeking refuge in this country,” said Steve Valdez-Symonds, Amnesty International UK's refugee and migrant rights director.
“No one should suffer such blatant exposure to prejudice and hostility, especially not in the form of highly insensitive remarks from the Home Secretary.
“The government's draconian asylum legislation is already set to tear apart legal protections in this country for refugees, victims of human trafficking and many other people, while Suella Braverman continues pouring petrol on a xenophobic and racist fire they themselves have lit.”