A series of amendments to a regulation on how internet traffic is managed in Europe were all rejected by MEPs.
Proponents of net neutrality, who demand that web traffic be treated equally by networks, have already criticised the move.
The existing legislation, which was accepted, will be developed into regulations.
Campaigners have said that provisions for protecting net neutrality in the existing text of the rules are too vague and many worry that it will be easy for internet firms to strike deals with content providers which may not be advantageous for everyone.
For example, it is thought that so-called "zero rating" agreements, in which customers can access certain sites and services for free outside their data plans, might become more widespread.
While this could be beneficial for those who want to access content from those providers, others worry that it will stifle innovation.
The rules, however, do stipulate that network companies will not be able to offer or market paid-for access to "fast lanes". Traffic management, they add, should be based on objective technical requirements.
Although some campaigners had suggested there might be growing support for the amendments within the parliament, all were voted down in large majorities.
It is thought that many MEPs would have been reluctant to begin a process of amending the regulation given that it might have delayed another aspect of the rules - the abolition of mobile data roaming charges.
The result is "hardly surprising" according to legal expert Chris Marsden at the University of Sussex, given that many of the major parties represented in the parliament all supported the regulation text without amendments.
The Body of European Regulators (BEREC) would now have nine months to issue guidelines to bodies like Ofcom in the UK, he added.
"So, [by] September next year we will have the guidelines and the real enforcement work begins," he told the BBC.
Dr Marsden also said there were still plenty of unknowns, such as what form regulations on "zero ratings" and fast and slow lane services might actually take.
There was also the issue of how laws in the Netherlands, Slovenia and Finland - which all have special net neutrality protections in place - would be affected.
Some initial guidelines, Dr Marsden added, would not be ready until 2016.
Michael Theurer, a liberal German MEP described the outcome as "regrettable" and added that he felt the regulations as passed do not include a clear definition of net neutrality to inform regulators.
Prior to the vote, the inventor of the world wide web Sir Tim Berners-Lee and a host of tech companies had expressed their support for the amendments and urged MEPs to vote them through.
Firms which has openly supported the amendments included:
"The fact is that what we use the internet for in 2015 is vastly different from those early days when Tim Berners-Lee was inventing the web," commented Chris Green of business consultancy Lewis as he pointed out that the rise of video streaming had placed extra burdens on network companies.
"Maintaining that information flow is an expensive process and the cost of running that infrastructure is falling on the shoulders of ISPs.
"For them, a two-tier internet makes much more sense," he told the BBC.
The idea that data should be ferried from place to place as quickly as possible, regardless of what it is, is how most people assume the internet works.
That's the essence of net neutrality.
However, it's possible to decide to prioritise certain types of data over others - perhaps, for example, by charging the producers of such data a fee to make sure their content gets delivered promptly.
For big video streaming sites, the prospect is worrying. They could find themselves coughing up lots of money in fees simply to give their users the same experience as before.
Some argue, however, that such fees are fair since it costs internet service providers a lot of money to keep providing such content, no matter how popular the streaming sites become.
Part of the problem with the rules in their current form, argued Joe McNamee at the European Digital Rights campaign group, is that they are ambiguous.
"As the text currently stands there is no indication as to how much abuse of dominance would be permissible under this arrangement," he told the BBC.
The sort of scenarios that could impact internet use include the creation of "fast lanes" and "slow lanes" or the creation of "zero ratings" in which some services may be accessed without using up any of the internet user's data quota.
In Belgium, for example,  some mobile phone companies currently allow unlimited access to Twitter and Facebook while all other data usage is part of a monthly plan. In a few countries such as the Netherlands, such practices are not allowed.
Besides a host of net neutrality campaigners, inventor of the world wide web Sir Tim Berners-Lee had added his voice to those supporting the amendments.
"If adopted as currently written, these rules will threaten innovation, free speech and privacy, and compromise Europe's ability to lead in the digital economy," he wrote in a blog.
And a string of tech companies signed a letter to the president of the European Parliament, Martin Schulz, asking MEPs to adopt the amendments.
The firms included Netflix, Tumblr, Vimeo, Kickstarter and Reddit.
"I was contacted by a number of start-ups and investors because they were deeply concerned about the impact of the European Parliament's network neutrality proposals on start-up innovation in Europe," Stanford professor Barbara van Schewick, who helped pen the letter, told the BBC.
Interestingly, three countries within the EU - Netherlands, Slovenia and Finland - already have a range of net neutrality rules enshrined in law.
These laws might have to be altered depending on how the new, EU-wide rules are interpreted by regulators later.
Elsewhere, net neutrality has received some regulatory protection in the United States after a vote in February this year placed new restrictions on what deals could be sought by internet firms with content providers.
But in other countries, such as India, "zero rating" is allowed.
"It's a fragmented picture across the board," said Dr Marsden.
"It's an extremely difficult area and there are probably no absolutely right answers."
The European Parliament has voted against a set of rules intended to safeguard "net neutrality" in the EU.