Liam Trotter struck as Millwall grabbed their second away point of the season and ensured Middlesbrough were held to a fourth successive league draw.
Barry Robson had put Boro ahead from 25 yards after Scott McDonald had chested the ball into his path for their first goal at home since August.
McDonald struck the post before Trotter headed home from close range after a scramble inside the Boro six-yard box.
Faris Haroun almost snatched the points for Boro but his header hit the post.
That came in the 95th minute after the substitute had connected with a cross from Marvin Emnes.
Boro are still unbeaten in the league this season and McDonald's strike against the Lions ended a sequence of three goalless draws.
The point took Boro to a landmark 11th game unbeaten since the start of the campaign, the best start since the club stepped up to the professional ranks in 1899.
But the draw was not enough to prevent Tony Mowbray's team from dropping down to third in the table.
The Lions had started the day in the relegation zone, but are now 21st, moving out of the bottom three on goal difference.