EU governments and lawmakers now have three months to either approve or reject the committee's decision, before the rules can be adopted by the EU executive as law.
"In all likelihood the measure will be adopted by member states and EU parliamentarians, even if we expect a lively debate in the European Parliament," one EU diplomat involved in the negotiations said.
The Commission, industry and exporting countries argue the 0.1% threshold is needed to avoid a repeat of supply disruptions in 2009, when US soy shipments to Europe were blocked after tiny quantities of unapproved GM material were found in some cargoes.
The limit "addresses the current uncertainty EU operators face when placing on the market feed based on imports of raw materials from third countries," the Commission said in a statement.
The EU imported more than 51 million tonnes of animal feed last year, worth almost €15 billion euros, according to Commission trade statistics. About half was GM soy from Brazil and Argentina developed by US biotech company Monsanto.
Green groups accused the EU executive of caving in to GM-industry lobbying by reversing its "zero-tolerance" policy on unauthorised crops. Some environmentalists argue that the effect of consuming GM crops is unknown and say these have not completed the EU's safety assessment process.
They said the move was an unnecessary solution to a problem that does not exist.
"Weakening safety rules to appease the animal feed industry compromises human and environmental safety," said Friends of the Earth food campaigner Mute Schimpf.
But the head of EU feedmakers' association Fefac, Patrick Vanden Avenne, said the decision would "safeguard vital supplies of new crop protein feeds from South America to our EU livestock industry".
Earlier this month the same EU committee failed to reach the necessary majority to approve the rules, because of opposition from some countries, including France.
But on Tuesday France voted in favour, after the conditions that unapproved GM crops must meet in order for the threshold to apply were strengthened, sources close to the committee said. "The criteria are stricter now than originally envisaged," said another EU diplomat.
The GM crops in question must have been approved in a non-EU producing country and an EU authorisation request must have been lodged with the European Food Safety Authority (EFSA) for at least three months, the diplomat said.
"On top of that [...] EFSA must have given an assessment that the presence of GM products of 0.1% are not detrimental to health and environment," the diplomat added.
The 0.1% threshold will only apply to imports of animal feed and not human food, despite warnings from traders and exporting states that it is impractical and costly to separate global grain supplies into those destined for humans and those for animals.
A majority of EU governments are reported to be in favour of a similar threshold for food imports, but a Commission source said on Tuesday there were currently no plans to draft a similar proposal for food for human consumption, but that it would "monitor the situation closely".
(EurActiv with Reuters.)