Tony Mowbray's side slipped out of the top six for the first time since October prior to kick-off following Brighton's win over Burnley, and Boro's performance did not match that of a side striving for promotion to the Premier League.
However, Millwall, who had lost their last five in the npower Championship, did not look like a side struggling for form as they dominated throughout in a thrilling encounter.
An own goal from defender George Friend and Lions midfielder Martyn Woolford's strike sealed a first away win for Kenny Jackett's side since November with Curtis Main pulling one back for the hosts.
Kieron Dyer and striker Main were the only changes to the Boro side that drew a blank at Burnley in midweek while Jackett recalled five players including Benik Afobe, Alan Dunne and skipper Danny Shittu following their 5-1 defeat at home to Peterborough last time out.
The first real chance arrived on 15 minutes when Karleigh Osborne tripped Main on the edge of the box. Grant Leadbitter took the kick and Jason Steele was struggling to get across as it narrowly flew over the crossbar.
Main was appealing to referee Michael Naylor again shortly after when he went down under pressure from Dunne inside the penalty area. Naylor waved away the protests as he became increasingly unpopular with the home supporters.
His reputation did not improve when the Lions, virtually straight after the incident, took the lead on 25 minutes. James Henry delivered a pin-point cross from the left and an unfortunate Friend headed into his own goal under pressure from Afobe and John Marquis.
Friend, along with his team-mates, felt he was fouled in the build up, only adding to the now toxic atmosphere inside the ground.
However, Boro almost replied immediately when Main met a Leadbitter corner full only to see his powerful header well blocked on the line by Nadjim Abdou.
The visitors looked rattled by Middlesbrough's response and goalkeeper David Forde almost gifted them an equaliser when he spilled a cross only for Mark Beevers to again clear off the line.
But Kenny Jackett's side took full control five minutes before the break when Jason Steele pushed Afobe's original effort into the path of Woolford who enjoyed the simplest of finishes to double the advantage.
Boro tried to rally a response after the break following the introduction of Ishmael Miller and Mustapha Carayol, and it was the latter who tested the reflexes of Forde on the hour mark as the Republic of Ireland international made a smart stop at his near post.
A goal was coming, though, and Friend went some way to making amends when he skipped into the area on 75 minutes before pulling the ball back for Main, who tapped into an empty net from six yards.
That strike clearly energised them as Main fired a golden opportunity wide with five minutes remaining before late drama erupted deep into stoppage time when substitute Scott McDonald's apparent equaliser was ruled out for offside.
A melee ensued and referee Naylor was almost caught in the middle of it before bringing the game and Millwall's slump to an end, condemning Boro to a seventh league defeat in their last nine outings.