The Teessiders needed a win to keep their Championship play-off hopes but were unable to do so as the Foxes booked their place in a play-off semi-final following five straight wins.
Middlesbrough’s Australian goalkeeper Jones was handed a straight red car for bringing down Leicester’s Lloyd Dyer with six minutes remaining.
At the time the score was 1-0 but Boro had a chance to get back in the match when New Zealand international Chris Killen had a spot-kick in the 71st minute but he missed and Leicester remained in front.
They then went ahead when Richard Wellens converted his penalty which Jones was sent off for, ending Middlesbrough’s disappointing season.
Jones’ fellow Australia, Scott McDonald, played a full 90 minutes but had few chances.