King made amends for Fryatt's miss soon after, slotting in the first of his two goals.
At the other end, Steve Howard and Fryatt threatened but failed to work Federici in a rare Leicester attack.
After Mills' winner, there was still time for Royals keeper Adam Federici to deny Joao Moreno and Matty Fryatt.
Hull hitman Matt Fryatt missed chances but sub Emmanuel-Thomas squeezed in his first Cardiff goal to secure the win.
On-loan keeper Mark Bunn saved the resulting penalty and the Foxes held on to the lead given them by Matt Fryatt.
Despite the hosts enjoying the majority of possession, the Tigers created the game's first chance as Fryatt missed a presentable headed chance.
Foxes manager Nigel Pearson was rewarded for making four changes from the side that lost 3-1 at Ashton Gate, including recalling Howard and Fryatt.
Hull had been the more impressive side for much of the game with Matty Fryatt heading wide before Aaron Mclean's shot was parried away by Jason Steele.
After the former had given the home side the lead, his header provided Fryatt with an opportunity to immediately double the lead but the young forward's shot was saved by Wednesday keeper Lee Grant.
When Mills' header put Reading in front for a second time, Paulo Sousa's side were unable to come back - as in the dying stages Federici pushed away a headed effort from Moreno and then parried a Fryatt shot.
The first real moment of threat to Cardiff came after 28 minutes as Fryatt forced goalkeeper Tom Heaton to tip his effort around a post with Bothroyd called on to clear Gerrard's goal-bound header off the line from the resulting corner.
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