The 28-nation bloc’s executive Commission said the deal can go ahead because consumers will continue to have a wide choice of alternative communication apps to use.
Facebook runs its own mobile messaging service with its Messenger app but the EU found the merged entity “would continue to face sufficient competition”.
EU competition chief Joaquin Almunia said: “While Facebook Messenger and WhatsApp are two of the most popular apps, most people use more than one communications app.”
The Commission said WhatsApp - launched in 2009 - has 600 million users globally.
Facebook chief Mark Zuckerberg hopes it will reach a billion in a few years.