Boro's U23s missed out on the chance to gain ground on the league leaders as West Ham came out on top of an end-to-end encounter and moved to the summit of the PL2 Division 2 table.
Rumarn Burell returned to the starting XI for Graeme Lee's side after a goalscoring turn off the bench in Monday's 3-2 victory up at Sunderland. Jack Robinson was the only other new face from four days ago, replacing Isaiah Jones.
Boro's youngsters knew that victory on the night would move them level on points with the visiting Hammers as well as first-placed Manchester United, who wait to play on Monday.
But the Teessiders knew it would be no easy feat against a West Ham side who boasted an impressive 14-game unbeaten run heading into the game.
Sure enough, it was Hammers winger Nathan Holland who made the breakthrough, curling in with just over 20 minutes played. The goal was just reward for a bright start for the away team, who attacked with poise and purpose and had seen Holland and Anthony Scully go close in the early stages.
An own goal briefly brought Boro back on terms a quarter-of-an-hour later, Harrison Ashby powerless to prevent turning captain Paddy Reading's cross past his own keeper as the defender looked to clear from the path of the lurking Burrell.
Then the London club regained the upper hand just before the break, Holland turning provider with a smart square pass when clean through, allowing Scully an easy finish.
Boro emerged for the second half with renewed purpose, and a goal from Daniel Dodds restored parity with 51 minutes played, the full-back connecting with Stephen Wearne's cross at the back post.
Just two minutes later, Lee's team led for the first time on the night, Sam Folarin curling in with aplomb after Boro pounced on a stray pass.
But the Hammers hit back with fifteen to play, Scully the man to bring his team level again with a close-range finish on the rebound.
And the East Londoners struck again with just over five minutes remaining, Holland providing another assist. The winger worked it in from out wide and Dan Kemp applied the finish.
Boro pushed on for a third equaliser, and a glancing header from Burrell in injury time wasn't too far off target.
Boro: Flatters, Dodds, Wood, Dale, Robinson (Gibson), Reading (c), Hackney, Malley, Wearne, Folarin, Burrell. Subs: Swan, Reed, Hood, Balde.
West Ham United: Anang, Rosa, Ashby, Cardoso, Longelo, Coventry (c), Kemp (Appiah-Forson), Lewis, Powell, Holland, Scully. Subs: Parker, Hegyi, Parkes, Hannam.