GB finished as runners-up in the overall table for the second successive Games following a total of 124 podium places: 41 gold, 38 silver and 45 bronze.
The men’s wheelchair basketball team clinched the country’s penultimate medal in Japan by defeating Spain 68-58 in their third-place play-off.
Gaz Choudhry was once again GB’s top scorer, registering 19 points, with Terry Bywater adding 14.
Krysten Coombs then had the final say with the shuttlecock.
He bounced back from Saturday’s semi-final loss to second seed Krishna Nagar by coming from a game down to beat Brazil’s Vitor Goncalves Tavares 12-21 21-10 21-16 in the SH6 bronze medal match.
Earlier, six-time Paralympic gold medallist David Weir finished fifth in the men’s T54 marathon in a season’s best time of one hour, 29 minutes and 45 seconds.
Fellow Briton Johnboy Smith was 10th in 1:32:25, while compatriot Derek Rae crossed the line ninth in the T46 race in 2:47:04.
Switzerland’s Marcel Hug won the T54 event in a time of 1:24:02, 20 seconds ahead of Chinese athlete Zhang Yong, with American Daniel Romanchuk third.
Weir said: “I’ve gone under 1:30 which I haven’t done for a few years, so I’m pleased with that.
“I knew it would be quick at the front but I am disappointed because I thought I was going to get a bronze medal today. But I tried my best, it just wasn’t quite enough.
“Credit to them, they (top three) were on another level.”