The tie is evenly poised. Middlesbrough were full value for their win at the Riverside Stadium and should have built a stronger lead.
Yet Roma, before their own fans, will start favourites to progress.
Middlesbrough recalled Dutch international Jimmy Hasselbaink and England prospect Stewart Downing to their attack.
Roma arrived at the Riverside Stadium ranked as one of the best teams in Europe. Only an equaliser by Inter Milan at the weekend had ended a record-breaking run of 11 successive wins.
Middlesbrough were awarded their debatable penalty after only 11 minutes. Brilliant skill by Gaizka Mendieta set Hasselbaink free inside the penalty area. Hasselbaink crashed into Gianluca Curci and the French referee, Elain Sars, pointed to the spot.
Curci raised his arms in bewilderment and it certainly looked as if Hasselbaink "had won the spot kick".
Yakubu enhanced his reputation as Boro's leading scorer by sending Curci the wrong way for his 19th goal of the season.
Mendieta will no be looking forward to a return to the Olympic Stadium. The former Spanish international had a disappointing season with Lazio, who share the stadium with Roma. Mendieta will no doubt be eager to prove a point.
Boro looked the most threatening side in the first half, with Roma failing to pose any problems in attack.
Steve McClaren rates Roma as one of the best sides in Europe but the visitors failed to live up to their reputation at the Riverside.
Lee Cattermole, an outstanding Middlesbrough prospect, fired wide for the hosts after the break. Roma then began to apply pressure in a bid to turn the game round. Yet they lacked a cutting edge and Boro checked them with their first-time tackling.
Alessandro Amantino was not far off target just after the hour with Roma's best effort of the game while at the other end Curci saved on his knees from Hasselbaink.
Middlesbrough introduced Mark Viduka for Yakuba nine minutes from time and the Australian international created a glorious chance with his first pass.