Western countries have already been supplying insurgents with what they call “non-lethal” equipment but the new decision marks a turning point in EU's support of the militants.
Extremist groups have swelled the ranks of insurgents in Syria and EU’s decision to arm them will lead to further insecurity which may come to haunt the West on their own doorsteps.
The grueling 12-hour talks to arm militants were marked by deep divisions and acrimony between champions of the move, namely Britain and France, and other reluctant partners.
"It was not possible to find a compromise with France and Britain," said Austrian Foreign Michael Spindelegger, a longtime outspoken opponent of the move.
Austria, Sweden, Finland and the Czech Republic were reticent about pouring more arms into a conflict that has already cost some 94,000 lives.
To send arms is "against the principles" of Europe which is a "community of peace", said Spindelegger.
The decision risks wrecking a US-Russian peace initiative which it is hoped both the Syrian government and opposition figures will attend, to take place in Geneva in June.
But it exposed desperation on the side of the West to turn the tide in the fast changing dynamics of the conflict, where the Syrian army is pushing insurgents to the corner.
The deal made in Brussels leaves the decision to supply arms to the rebels up to each nation.
British Foreign Secretary William Hague said that Britain, while championing the move, had "no immediate" plans to supply weapons to the rebels.
"None of the member states have the intention of actually providing arms at this stage," said Frans Timmermans, the Dutch minister who tried to steer a compromise.
"Member states will have to decide for themselves in the future whether they will provide groups with arms in that region."
But a written vow to respect a joint moratorium on supplying arms until after the planned peace conference in Geneva next month was eliminated in the final deal.