Despite opposition from the Liberal Democrats and former Cabinet minister Tom Watson, the bill passed through the committee stage with help from the Conservative party.
After two hours of debate during its third reading, the legislation was voted through by 189 to 47 shortly after midnight.
However, culture secretary Ben Bradshaw was forced to ditch clause 18 of the bill, which would have enabled large-scale new powers to block offending websites.
The measure was instead amended in clause 8 to give the secretary of state power to get an injunction against "a location on the internet which the court is satisfied has been, is being or is likely to be used for or in connection with an activity that infringes copyright".
Bradshaw also removed clause 43 of the bill, which pertained to orphan works by photographers and would have enabled the commercial use of images without the copyright holder's direct consent.
During the controversial bill's second reading in parliament, clauses giving greater regulatory powers to Ofcom and enabling the independently funded news consortia (IFNC) scheme were ditched following opposition from the Tories.
The government also dropped its proposal for a 50p monthly levy on all UK landlines to help fund the rollout of high-speed broadband networks.
However, the bill's new powers to cut off the internet connections of persistent online copyright pirates in a 'three strikes' process were voted through without amendment.
Various MPs complained, though, that the bill was too important and contentious to be rushed through in the 'wash-up' stage before parliament is dissolved.
The digital economy bill will now transfer to the House of Lords, where the new amendments will be voted in before becoming law.