The Dutch striker took his tally for the season to 14 with a first-half brace to sink shot-shy Millwall.
The Teessiders had slipped out of the Championship play-off spots after a run of seven games without a win, but they followed up last week's victory over Nottingham Forest - their first in 2012 - with another valuable three points.
Millwall had scored just once in the league at home since November and did not remotely look like adding to that tally until Darius Henderson struck against the run of play before half-time.
But they could not find a leveller despite a spirited second-half performance, and a late strike from substitute Curtis Main condemned them to another defeat.
Boro could have been three up in the opening five minutes but for some wayward finishing.
First Millwall failed to deal with Jason Steele's long goal kick and Lukas Jutkiewicz fired narrowly wide.
Moments later Jutkiewicz's scuffed effort in front of goal was clawed away by David Forde and from the corner, Emnes headed Barry Robson's cross over.
Forde, who was dropped for Saturday's FA Cup defeat by Bolton, also tipped a looping Jutkiewicz header over the top as the visitors dominated the opening stages.
The goal they had been threatening duly arrived in the 14th minute from another Robson corner.
The unmarked Rhys Williams hooked the ball back towards goal from the corner of the six-yard box and Emnes deflected it past the unsighted Forde.
While there was a touch of fortune about Emnes' first goal, there was nothing lucky about his second in the 38th minute.
Emnes collected Robson's pass 35 yards out, skipped past Harry Kane's challenge on the edge of the area and thumped a superb low shot past Forde.
But five minutes later Millwall, who had not managed a single effort on goal, suddenly grabbed a lifeline.
Scott Barron floated a free-kick into the area, Liam Trotter nodded it back across goal and Henderson looped his header over Steele and into the net.
Lions boss Kenny Jackett made a double substitution at the break, throwing on Alan Dunne and Jimmy Abdou, and his side improved in the second half.
However, Liam Trotter could not take advantage of a defensive mix-up and fired over, Henderson headed wide and Steele saved from Kane and Liam Feeney.
And Boro wrapped up the points four minutes from time when Julio Arca crossed and teenager Main crashed a powerful shot past Forde and high into the net for his first Boro goal.