The 26-year-old central defender has followed goalkeepers Richard Strebinger and Raphael Wolf into the club as they look to make up for losing Tim Wiese, Claudio Pizarro, Mikael Silvestre and Marko Marin.
Lukimya-Mulongoti has put pen to paper on a three-year contract after joining for an undisclosed fee.
"We are delighted to have been able to convince Assani to join Werder Bremen," said the club's director of sport Klaus Allofs.
"He has impressed with good performances with Dusseldorf and is one of their best players.
"His physical strength and his pace and tackling ability will give more stability to our defence."
Lukimya-Mulongoti said he needed no convincing to join Bremen.
He added: "As soon as I heard of their interest, my mind was made up quickly," he said.
"I had a great time with Fortuna and I shed a few tears to leave there, but as a footballer, you want to improve yourself and when every individual player at another club has more quality, then that also helps you to grow.
"I have absolute faith in my ability, otherwise I would have taken a different decision.
"You need a good competition for places and I am ready to face up to that from the first day."
Meanwhile, Bremen have extended the contract of goalkeeper Sebastian Mielitz by a year until 2014.
"I have the chance of being the number one here at my club and I have worked hard for many years for this," he said.
"I know what I am capable of and I am confident enough to reach this goal."