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.
The Lions 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 Benik 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 Grant 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 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.
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.