Despite 53 from Joe Cuthbertson, 29 by Kieran Donnachie and 26 from Arsh Gupta, Thornes ended on 165-9 in reply to 170-8 in a 32-over semi-final.
James Donnachie was the pick of the Wakefield bowlers with 3-29.
There was more disappointment for Thornes in Saturday’s Yorkshire Southern Premier League match against Hallam as they went down by two wickets.
Hallam’s victory had not looked likely when Thornes, having elected to bat, had reached 131-1, as their top three all looked good with Byron Boshoff hitting 58, Kieran Donnachie 55 and Matt Jordan 51.
But after that, only Matty Taylor reached double figures - scoring an unbeaten 30 - as Robert Heyes and Harnan Puni claimed three wickets each, Wakefield ending on 218-8.
Alex Hughes got Hallam off to a decent start and they reached 124-2 before he fell to Brad Green. A wobble then reduced the visitors to 130-5, but Jamie Stone added 41 with Robert Heyes for the sixth wicket to steady the ship and he stayed firm as two more wickets fell before Charlie Bourne arrived to finish the job with an unbeaten 16 in 12 balls.
Hallam reached their target with five balls to spare despite Daanyaal Ahmed taking 3-58.
Wakefield Thornes seconds did bring some cheer to the club as they moved up to seventh in Division One with a six-wicket success against Hallam seconds.
The bowlers paved the way for the win as they dismissed Hallam for just 99. James Donnachie claimed 3-20, Junaid Yousaf 3-30 and Jawad Akhtar 3-14.
Thornes did lose four wickets in their reply, but they were brought home in 33.3 overs by Jonathan Scott (33no).