The opening 45 minutes saw both sides struggle to create many clearcut chances.
Middlesbrough's best fell to McDonald with seven minutes played but he shot over the bar from the edge of the box, while up the other end Grant Leadbitter got back to block an effort from Karl Henry that looked to be heading in.
Wolves then began to dominate the contest, but they were unable to breach the home goal.
Their failure to do so was punished three minutes from time when Stephen Ward was adjudged to have handled inside the area. Emnes stepped up to convert the resultant penalty and in doing so put his team in front.
The points were sealed deep into stoppage time when McDonald caught Wolves on the break and sent an effort beyond the reach of Ikeme.