Returning after injury were Lee Cattermole and Tony McMahon, while Malcolm Christie got another 75 minutes under hs belt.
It was Christie who gave Boro the lead less than 10 minutes into the second half, but the lead lasted less than 10 minutes as Leeds hit back through Jonathan Howson.
Both sides had opportunities to win it, Boro with two good chances in the last five minutes, but it finished 1-1.
It ended a fine season for the Reserves who have been in the top two or three all season but they just couldn't keep pace with runaway leaders Manchester United. They remain third for the moment but could be beaten into fourth if Manchester City win their final game.
Boro side:
Knight, McMahon, Grounds, Cattermole (Owens), Davies, Wheater, Liddle, Kennedy, Christie (Hutchinson), Craddock, Johnson