Balogun who joined Wigan on loan from Brighton and Hove Albion was introduced in the 64th minute, after teammate Cheyenne Dunkley was sent off two minutes earlier.
Wigan took the lead in the 29th minute but Middlesbrough took advantage of their numerical strength, scoring two goals in four minutes through Lewis Wing in the 64th and 68th minutes.
And in the 76th minute an own goal by Harold Moukoudi saw Wigan draw level at 2-2.
Efforts by Middlesbrough to find the winner proved abortive as they could not breach Wigan’s backline involving Balogun, again.
Following the draw, Wigan remain in the relegation zone in 22nd position on 30 points and are temporarily four points away from safety.
And in another Championship game played on Tuesday, Queens Park Rangers held Swansea to a 0-0 away draw.
QPR paraded Nigerian duo, Eberechi Eze and Bright Osayi-Samuel.
With the statement at Swansea, QPR are now winless in their last five league games, losing four and drawing one.
They are currently 17th on 39 points in the 24-team Championship league table.
By James Agberebi