Scientists applauded and celebrated a "new era in particle physics" as the beams collided in the Large Hadron Collider at the European Organisation for Nuclear Research in Geneva.The head of the Atlas team, Fabiola Gianotti said the team is delighted.
"We got something like 40 events per second, which is the expected rate," she said.
"It's the beginning of a new era of physical exploration."
Two earlier attempts at collisions had failed.
The first beams were lost when a power supply tripped, and the second try was hampered by a problem with the new magnet protection system.
Two beams of protons began 10 days ago to speed at high energy in opposite directions around the 17-mile tunnel under the Swiss-French border at Geneva.
The beams have been pushed to 3.5 trillion electron volts, the highest energy achieved by any physics accelerator.
Scientists have now managed to force the two beams to cross, creating collisions and showers of particles.
They will continue to attempt collisions, starting a new era of scientific research.
The aim is to find the much talked-about Higgs boson particle which is thought to play a key role in the structure of the Universe, and would help scientists explain why matter has mass.
Detractors fear the collisions will create black holes that could swallow the earth.
However, the scientists say the holes will not be powerful enough to bring mankind to a premature end.
The LHC created a sensation when it was launched in 2008, with fears that it would lead to the end of the world, but technical faults put it out of action for a year.
A faulty electrical connection between two of the accelerator's magnets caused the system to fail.
It suffered another setback in November 2009 when a "bit of baguette", thought to have been dropped by a bird, fell onto machinery and caused a fault.
Conspiracy theorists had claimed the machine is aware of its own power and is deliberately breaking down to avoid the destruction of the universe.
The $10bn project has been described as the world's largest scientific experiment.
Thanks to SKY News
