Despite a season blighted by injury, the 2017 world champions skated a lyrical, moving programme for a season's best 155.60 (234.84 combined), drawing a packed crowd to its feet with their clean jumps and gorgeous lifts.
"This has been a difficult year for us, we've had injuries and other issues," said Sui, who laughed as Han pumped his fists at the end of the routine.
"But our coaches and team gave us support that we were able to turn into strength."
Russians filled out the rest of the podium with second place going to Evgenia Tarasova and Vladimir Morozov after a regal but mistake-marred programme that included the latter putting his hand to the ice in the wake of their Triple toe loop.
"In the free programme it was tough and we had to fight for every single element," Morozov said after their routine, which garnered a season's best 147.26 for a total of 228.47.
"It was totally different to yesterday, we were struggling to get everything right."
Wenjing Sui and Cong Han of China celebrate after the Pairs free skating during day 2 of the ISU World Figure Skating Championships 2019 at Saitama Super Arena on March 21, 2019 in Saitama, Japan
Image credit: Getty Images
Third place went to Natalia Zabiiako and Alexander Enbert, whose dynamic programme earned them 144.02 and a combined total of 217.98.
European champions Vanessa James and Morgan Cipres, favourites going into the worlds after an undefeated season, were only able to manage fifth.
Frenchwoman James collided with Italian skater Matteo Guarise during warm ups for the short programme on Wednesday and fell after a botched landing in their routine.
"Worlds hasn't been our best friend, I fell on the twist in the short programme once and I fell on the triple Salchow before, but we know that each time we are getting stronger," said Canadian-born James.
Cipres echoed her determination.
"I think we did our job today and we are never giving up. We won't give up until we get the world title."
The World Championships continue at the arena north of Tokyo until March 23, with the most-watched contest - the men's singles - beginning later on Thursday.