The hosts paid the price for the missed opportunities, and after scoring the first 15 penalty kicks, United’s Anthony Ilanga missed a kick, sparking celebrations among 9,000 Middlesbrough fans.
Gidon Sancho’s goal in the 25th minute, shortly after Cristiano Ronaldo missed a penalty, was a small reward for United, who dominated the match and missed Ronaldo and Marcus Rashford golden chances.
Middlesbrough held on until they equalized in the 64th minute through former United rookie Matt Crooks with a close-range shot to the goal.
Bruno Fernandes hit the post and the rest of United’s attempts in extra time were unsuccessful.
Middlesbrough showed ingenuity in the penalty shootout to overthrow the 12-time Cup champion.