Mateen, 32, wore a ceremonial uniform while his 29-year-old bride was in a long white dress and sparkling jewels for the event at the sprawling Istana Nurul Iman palace.
They made their first public appearance as a married couple in a procession through the normally sleepy capital Bandar Seri Begawan in front of thousands of onlookers.
The popular prince was one of Asia's most eligible bachelors until he tied the knot with Yang Amat Mulia Pengiran Anak Isteri Anisha Rosnah, who is from a prominent family in Brunei.
Mateen's father is Sultan Hassanal Bolkiah, the world's longest-reigning monarch and once the richest man on the planet.
There was a festive atmosphere in the city with free ice cream on offer and soft drinks for sale as people began to take positions along the parade route hours before it began.
Wearing a traditional formal outfit and matching songkok hat, retired banker Haji Suhaimin Abas, 66, was among the elite Bruneians to receive an invitation to the wedding ceremony.
"This is a very big celebration," he told AFP as he ate breakfast before going to the palace.
Royalty from Jordan, Saudi Arabia, the United Arab Emirates, Bahrain and Bhutan were listed among the reported 5,000 guests.
Malaysian Prime Minister Anwar Ibrahim, Indonesian President Joko Widodo and Philippine President Ferdinand Marcos were among government leaders in attendance.
'Once-in-a-lifetime moment'
Sunday's celebration is the highlight of 10 days of pomp and pageantry in the tiny country, whose extreme wealth is derived almost entirely from its enormous oil and gas reserves.
Mateen, a British-trained military officer in Brunei's armed forces and a helicopter pilot, held court with his wife at the elaborate ceremony before invited guests.
The ceremony was steeped in tradition drawn from Brunei's centuries-old history as an Islamic monarchy.
The couple stood in the back of an open-top Rolls-Royce waving to onlookers as they weaved through the capital, where their images have been displayed on street arches and building facades for days.
Many of the sultan's subjects lined the streets under a scorching sun to catch a glimpse of the couple.
Hajah Aminah Abd Morsidee, 91, who has seen five royal weddings in her lifetime, said she was "happy to see Prince Mateen marrying the beautiful Anisha."
Schoolteacher Norliha Mohamad Din, 37, said it was a "once-in-a-lifetime moment."
"I have seen Prince Mateen since he was small," she said. "I'm very happy for him. This is one way of showing appreciation to the royal family."
As the 10th child and fourth son of the sultan, Mateen is unlikely to ever ascend the throne.
But he appears to have taken on the unofficial role of presenting a modern face for the royal family in a bid to connect with a younger generation of Bruneians raised on social media.
Mateen's matinee idol looks and well-chiseled body have earned him a massive following on Instagram, where carefully curated photos and videos show him playing polo, dabbling in photography and posing in military uniform.