Wigan, who gave Marlon King their £5million signing from Watford his debut, were hoping to end their miserable away form.
Middlesbrough soon impressed with their speed and movement off the ball as they put the visitors under strong pressure.
Sanli Tuncay was unlucky after a brilliant solo effort that ended with the Turkey international firing just wide.
Only the outstretched foot of Paul Scharner deprived Tuncay of a goal following a Downing pass from the left.
Tuncay followed up by shooting wide shortly after as the home side dominated the opening play.
An opening goal by Jeremie Aliadiere after 19 minutes was no more than the Teessiders deserved.
The former Arsenal striker collected a Downing pass on the left, moved into the penalty area and beat Chris Kirkland with a powerful shot.
It was Aliadiere's second goal for the club and only his third career Premier League goal after getting off the mark for former club Arsenal.
After 30 minutes Middlesbrough suffered a blow when Tuncay pulled up with a hamstring injury and was forced to leave the field, but after a three minute delay Mido stepped into the action.
Emile Heskey headed wide for Wigan, but on the balance of first-half play the home side should have held a commanding lead.
Early into the second half, Mido and Wigan centre-half Titus Bramble both went down after a clash of heads but fortunately both recovered quickly.
Wigan though began to pour on the pressure and Heskey headed wide from a corner.
Wigan substitute Jason Koumas took over from King, who had struggled to get into the game.
Middlesbrough were missing the penetrating runs of Tuncay and Wigan were now showing a greater sense of urgency and only a brilliant Mark Schwarzer save denied Heskey a headed equaliser.
The crowd tried to lift Middlesbrough at this stage as Wigan surged forward time and again in a desperate bid to save a point.
The visitors were the more threatening side in the closing stages and the final whistle came as a relief to the 22,000 home crowd.