If there are any future disputes about the use of such patents, they will be settled under the industry standard of Fair, Reasonable and non-Discriminatory (FRAND) practice.
The Commission said that as a result, any company signing a licence accord with Samsung will now be protected against SEPs injunctions.
(Also see: Samsung makes settlement offer as EU looks to end tech patent wars in Europe)
Protecting intellectual property is essential, EU Competition Commissioner Joaquin Almunia said, but it should not be "misused to the detriment of healthy competition and, ultimately, of consumers."
Samsung's commitment on SEPs "provides clarity to the industry on an appropriate framework to settle disputes over 'FRAND' terms in line with EU antitrust rules," Almunia said in a statement.
(Also see: Google deal no 'gentlemen's agreement', says EU antitrust chief)
"I would also encourage other industry players to consider establishing similar dispute resolution mechanisms," he added.
In a related case, the Commission said it had found Motorola Mobility at fault for abusing its dominant market position by pursuing a SEP injunction against Apple in a German court.
Motorola Mobility will now have "to eliminate the negative effects resulting" from the case, it said, without, however, imposing a fine.
(Also see: Google's antitrust deal with EU faces opposition)Patent holders should get a fair return but companies seeking to use them should also be able to do so on FRAND terms, Almunia said.