Jordi Gomez's fierce free kick in the 84th minute grabbed Latics a point after Grant Leadbitter added to a first half, George Friend equaliser following Grant Holt's penalty that gave Latics the lead in the first half.
Holt and Marc-Antoine Fortune both had penalty claims turned down in the first half for what looked like clumsy challenges but the referee waved play on both times.
Owen Coyle made three changes for the game as Jean Beausejour came in for James McClean, James McArthur came in for Ben Watson and Fortune replaced Shaun Maloney who missed out due to a foot injury.
Latics in the ascendancy with a penalty claim just seven minutes in as Fortune raced through on goal and was seemingly pushed to the ground by a trailing defender, no penalty said the referee.
A frustrated Latics pushed on from there and 10 minutes later a penalty was eventually awarded after Boro's equalising goal scorer Friend grabbed a handful of Fortune's shirt.
Holt stepped up to give goalkeeper Luke Steele the eyes, sending him the wrong way and blasting in the opening goal.
Six minutes later and another penalty not given as Holt battled to bring the ball down in the area, got in front of Jonathan Woodgate and was tumbled to the floor.
The frustration in the DW Stadium was building but Boro were beginning to create chances as Lukas Jutkiewicz forced Scott Carson to turn the ball low around his right hand post.
With half time approaching and the game opening up Boro equalised when a foul by James McArthur on Friend was waved play on down the visitors's left.
Friend stayed on his feet, advanced into the area and fired a low shot across Carson and into the bottom corner.
It couldn't have come at a worse time for Latics as they looked to be holding onto the lead.
The second half became even more action packed, first with James McCarthy poking the ball under Steele but not hard enough as it trickled towards the line with the goalkeeper diving on the ball to prevent a goal.
Moments later Carson was forced into a low save as Boro winger Albert Adomah rifled an effort from a tight angle.
Latics suffered a set back midway through the second half as Holt was forced off through injury.
With 15 minutes left on the clock Middlesbrough took the lead.
A high ball into the box aimed at Jutkiewicz wasn't dealt with by Emmerson Boyce and Leon Barnett and a loose ball fell to Adomah on the right of the six yard box with Leadbitter waiting in the centre to tap his side into the lead.
The pressure was on Latics and the changes came as Gomez and McClean caused Boro real problems.
Another addition Roger Espinoza gave Latics bite in midfield and with seven minutes left an interception from a slack Boro pass at the back saw the Honduran hacked down by Dean Whitehead and Woodgate.
Up stepped Gomez in the 84th minute shaping up for what seemed to be a precise finish but no. The Spaniard wasn't holding back and as the referee blew his whistle he hammered the ball left footed through the wall to bulge the back of the net with Steele stranded on his goal line.
At 2-2 both teams looked desperate to claim three points.
Fortune came close to latching onto the end of a Stephen Crainey cross and Beausejour hit the side netting in stoppage time.
Boro also had their chances as Emnes forced a sprawling save from Carson and then rippled the side netting moments later.
Following five minutes of stoppage time the referee blew time on a second 2-2 draw in the space of five days.