The Olympic bronze medallists finished with 331.41 points.
China's Chen Ruolin and Liu Huixia won the gold, building an unassailable points total of 356.38 by executing five nearly flawless dives.
The silver was a career-best international result for Benfeito and Filion.
''It feels great to get that medal,'' said Filion. ''We've overcome a lot of challenges over the years and to have back-to-back international successes is very rewarding.''
Chen's fourth straight world title in this event added to her four Olympic gold medals.
Malaysia's Pandelela Rinong and Mun Yee Leong were 0.27 points behind Montreal's Benfeito and Laval, Que., native Filion to claim bronze.
The Chinese were first through all five rounds while Filion and Benfeito appeared on track for third. But their final twisting dive earned them 81.60 points which tied them with the Chinese for the best dive of that round to overtake the Malaysians.
''After our third dive was a bit subpar we just told each other to dive like we do in practice,'' said Benfeito. ''The last two have been big point getters for us this year so we knew we could stay in the medal mix.''
Filion and Benfeito's bronze in London was their first big international success since placing third at the 2005 world championships in Montreal when they were teenagers. They were fourth at the 2007 and 2009 worlds and seventh in 2011.
''We are like sisters,'' said Filion. ''We know each other really well and work well together. We've gone through many challenges in our career and gained some valuable experience. It has allowed us to be consistent at this level for a long time.''
It is Canada's second diving medal of the competition and third overall. On Saturday, Jennifer Abel of Laval, Que., and Pamela Ware of Beloeil, Que., took bronze on women's three-metre synchro.
China won two golds Monday with Li Shixin also retaining his men's one-metre springboard title.
The victories re-established China's dominance after Germany had snatched a diving gold the Asian country was also expected to retain on Sunday.
"Our coach has been telling us that once we step down from the podium you start from zero," Chen said. "That's the attitude I have carried forward to help me win so many gold medals."
Chen and Liu never looked back after executing a polished backward pike to take an early lead. They nailed a forward pike with 3 1/2 somersaults for a finals-high 82.80 points to almost clinch the title with two dives left.
Chen has won her four world titles with different partners each time. She has had so many different diving mates that when asked to describe them she needed help to remember all their names.
She said her latest partner "is very young but very adaptable, so I find it very easy to work with her."
Chen won her first world title five years ago when she was just 15, the same age that Liu is now.
"I don't have as much experience as the other divers here," said Liu, who is a champion on her world debut. "But I have learned a lot from Chen Ruolin."
China has won gold in three of four diving events so far at Montjuic Municipal pool, with its picturesque views of the Catalan capital.
Earlier, Li scored 460.95 points from six dives after rallying from a poor start to give the world's pre-eminent diving power its fourth straight — and seventh of the past eight — world title in the men's 1-metre springboard.
"The competitors were so strong. That I can win this again, I am just so lucky," Li said. "When I was young my coach gave me a video about the Olympic Games in 1992. I remember I have a dream I can stand in this pool.
"So today my dream came true and I won the championship. I feel this pool is amazing. Actually, Spain is very lucky for me. Since 2005, I have been here seven times. It's like here is a second home town. In China, somebody called me 'King of Spain.'"
Four-time European champion Illya Kvasha of Ukraine took silver with 434.30 points, while Alejandro Chavez of Mexico earned bronze with 431.55.
The final was billed to be a battle between Li and Matthieu Rosset of France, who finished 0.5 points behind the Chinese diver in the preliminaries on Saturday.
Rosset entered the fifth round in the lead but blew his entry, allowing Li to take command by completing a difficult inward pike with 2 1/2 somersaults for a single-dive highest score of 86.70.
But with Kvasha pushing, Li still had to execute a tough forward pike with 3 1/2 somersaults on the last dive to ensure he won.
"My coach told me that I need to control myself," Li said. "I knew that in the last rounds I have the confidence that I can overcome everything."
Rosset, who was aiming for France's first diving medal at the worlds, finished in sixth place.
On Saturday, Wu Minxia and Shi Tingmao won the women's three-metre synchronized springboard. The next day, China's run of three consecutive world titles in the men's synchronized 10-metre platform was broken by German pair Sascha Klein and Patrick Hausding.