The defeat also means that there will be no more midweek Carling Cup games cluttering up the fixture list, despite the fact that we would have had a juicy home tie against Everton to look forward to had we won.
John Filan (Ankle), Steve McMillan (Groin), Geoff Horsfield (Flu) and Tony Dinning all got rested for the game, with Andy Liddell, Lee McCulloch, Peter Kennedy and Nathan Ellington playing less than the full-game.
This meant that Gary Walsh got his chance in goal, Leighton Baines came in at left back, Peter Kennedy filled in on the left flank with McCulloch being pushed up front alongside Neil Roberts.
Andy Liddell started on the right wing with Eaden behind him. Jarrett and Bullard filled the centre midfield spots, Breckin and Jackson were the centre backs.
A goal in each half from Massimo Maccarone and Gaizka Mendieta was enough for the Premiership outfit to squeeze into the next round, but they were rattled by a Wigan display that deserved more than a disappointing defeat.
And when midfielder Jimmy Bullard thundered home a free-kick with 15 minutes to play the home fans were preparing for a grandstand finish from the first division high-flyers.
Wigan can look back on a number of missed chances, especially in the first half, as they let their opponents off the hook. Both Lee McCulloch and Neil Roberts squandered before the interval, with McCulloch bringing a tremendous save from Boro keeper Mark Schwarzer.
But the visitors led at the break after Danny Mills beat three men and hit a shot that appeared bound for the arms of home keeper Gary Walsh, only for Maccarone to deflect it in.
The home pressure continued after the break and Jason Jarrett amazingly fired wide after Peter Kennedy's perfect cross caused havoc in the visiting defence.
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Far from knocking the stuffing out of the home side, they came back with a vengeance and Bullard's free kick set up a tense finish, but the Premiership outfit held on.
'Boro boss McLaren said: "Full credit to Wigan, who gave us just the type of game I was anticipating," he said.
"It was a very tough draw to come here but we dug in, we worked hard and we showed the quality where we needed it.
"We didn't fold under pressure and we got the breaks at the right time and hung on at the end."
Meanwhile Jewell commented: "We could have got a little ragged when we went 2-0 down, but we kept going and it is a testament to our performance that the Boro players were so delighted to hear the final whistle.
"All in all it was a good display, but just not the ideal result.
"Boro have got some quality players, but we gave them a real scare and we didn't look out of place out there at all."
Leighton Baines had a stormer at left back, and it was a shame that his volley cannoned off Greening before Mendieta scored their second.
Jarrett looked impressive in the middle of midfield and should replace Tony Dinning for Saturday's game against Crystal Palace after the former Wolves midfielders poor form of late.
We lacked that spark upfront however, that little bit of creativity which the Duke is so capable of. Jewell knew this and introduced the striker midway through the second half.
The leading scorer didn't seem to concerned with the game and just happily seemed to watch the clock tick down until it was home time.
Otherwise it was a typical Latics performance and we were unlucky not to get something, at least force extra time.
Personally, mind, I feel that Jewell did not want to win this one.
He was not his usual self when we were trailing, he is normally the most animated man in the stadium, not last night.
I believe he also rested many of his first teamers who have been playing two games a week for a number of weeks now, and the tiredness has started to show on the small squad.
He didn't wear his lucky trainers either! Instead he smartened himself up, with shoes and pants on.
I don't mind though, I agree with the ploy. The league is the most important thing, and the league results we're getting hampered by the sheer volume of games being played.
Everton at home would have been very nice though.
Wigan Athletic:
Walsh 6
Baines 8
Breckin 7
Eaden 6
Jackson 7
Bullard 7
Jarrett 8
Kennedy 7 (Flynn 4)
Liddell 7 (Teale 7)
McCulloch 6 (Ellington 3)
Roberts 6
Middlesbrough:
Schwarzer 7
Mills 5
Queudrue 6
Riggott 7
Southgate 7
Boateng 7
Greening 5
Juninho 7
Mendieta 7 (Zenden 5)
Maccarone 6(Nemeth 3)
Ricketts 3 (Doriva 7)
External Reports
The Guardian
Manchester Evening News
Ic Teeside
This is the North East.
Teamtalk.