The Sky Blues suffered a 1-0 defeat at the Riverside Stadium despite a well fought performance.
Andraz Sporar's second half strike in the 58th minute was enough to see off Mark Robins side, although the Sky Blues came close to scoring throughout the game and almost took the lead just after the break when Kyle McFadzean's effort cannoned off the crossbar.
The Sky Blues applied the pressure on the hosts in the early stages of the game, just six minutes in smart play from Callum O'Hare saw him lay the ball neatly to Jordan Shipley on the edge of the area, but he fired just wide.
Just minutes later O'Hare and Josh Eccles played good football down the right before Viktor Gyokeres set up Eccles, whose driven effort went just wide of Joe Lumley's post.
The hosts' first chance came 11 minutes in when Sporar created some space inside the area, his shot was heading for the far corner before a good block by Dom Hyam kept the game goalless.
Middlesbrough then came close through Brighton loanee Aaron Connolly who managed to drive into the area before his effort was well handled by Simon Moore. Moore was on hand again on the half an hour mark to keep the game level, after a free kick just outside the area was back-heeled and Sporar hit a powerful effort towards goal, but Moore made a solid stop.
City had another chance to take the lead on the 36th minute after Shipley's floating corner was met at the back post by Kyle McFadzean, however his effort went the wrong side of the post.
Mark Robins' men had the best chance to open the scoring just before the break, nice link up play saw Eccles find O'Hare with space inside the area, however his first time effort was well kept out by Lumley as the sides went in level at the break.
HALF-TIME: MIDDLESBROUGH 0-0 SKY BLUES
The away side started the second half brightly, and in the 52nd minute, a well delivered corner by Shipley was headed into the path of McFadzean, who took a touch and smashed his effort into the bar.
Middlesbrough made a double change bringing on Folarin Balogun and Martin Payero 56 minutes in, and just two minutes later Balogun's run down the left saw him cross the ball across the six yard box for Sporar to tap home making it 1-0.
City nearly replied immediately to Middlesbrough's goal, a whipped cross by Eccles was well met by O'Hare whos glancing header forced a good save out of Lumley.
Paddy McNair came close to doubling the hosts lead after he was on the end of Marcus Tavernier's corner, however he was denied by the post.
The visitors kept battling and Gyokeres had a chance to level the game on the 76 minute mark, good link-up play between O'Hare and Ben Sheaf saw Sheaf play a through ball to Gyokeres, but after driving into the area, his effort couldn't find a way past Lumley.
Despite late pressure from City, they were unable to score past the hosts and ended up suffering a 1-0 defeat.
FULL TIME: MIDDLESBROUGH 1-0 SKY BLUES
Yellow Cards: Jordan Shipley (64'), Neil Taylor (91'), Joe Lumley (93')
Attendance: 22,940 (1,280 away supporters)
Sky Blues XI: Simon Moore (GK), Josh Eccles, Dom Hyam, Kyle McFadzean (C), Jake Clarke-Salter, Jake Bidwell (Ian Maatsen 76'), Jordan Shipley (Martyn Waghorn 68'), Ben Sheaf, Jamie Allen (Gustavo Hamer 63'), Callum O'Hare, Viktor Gyokeres.
Unused Subs: Ben Wilson (GK), Michael Rose, Julien Dacosta, Ryan Howley.
Middlesbrough XI: Joe Lumley (GK), Anfernee Dijksteel, Neil Taylor, Dael Fry, Marcus Tavernier, Andraz Sporar, Jonny Howson (Martin Payero 56'), Paddy McNair, Matt Crooks, Aaron Connolly (Folarin Balogun 56').
Unused subs: Luke Daniels (GK),Lee Peltier, Duncan Watmore, Sol Bamba, Josh Coburn.