The victory checked an alarming slide down the table following relegation from the Premier League last season. Whether it can lead to a promotion play-off challenge remains to be seen.
Middlesbrough gave a more enterprising display after a number of lack-lustre performances and should have won by a bigger margin.
Scunthorpe, however, were desperately unlucky to play for 80 minutes with only ten men.
Cliff Byrne was sent off in the opening minutes when the referee ruled he had fouled Jeremie Aliadiere. The penalty was a harsh decision but, having awarded it, the referee had no alternative but to dismiss Byrne as the last man.
England under-21 international Adam Johnson made no mistake from the spot to record his tenth goal of the season.
After that the outcome of the game was never in doubt. Middlesbrough certainly dominated the first half and should have piled on the goals.
Boro dominated from then on, with Johnson striking a post and Tony McMahon flashing a shot wide.
Scunthorpe were putting up a dogged defensive display but a second goal was almost inevitable and Rhys Williams provided it with a well-drilled left-foot shot from the edge of the penalty area.
Middlesbrough piled on the agony for Scunthorpe a minute after the break when Aliadiere marked his return to the side with a goal.
Danny Coyne, recalled in goal by Middlesbrough, saved from Grant McCann as the visitors attempted to reduce the arrears.
There was a shock development for Boro fans in the closing minute though. A linesman had spotted an offence by striker Leroy Lita in the penalty area. He brought it to the attention of the referee who then flashed a red card.
There was no festive cheer for Scunthorpe but Middlesbrough could take heart from an improved performance, especially with the next home game against Manchester City in the FA Cup in the new year.