It's a big blow as Latics were quietly confident the appeal, backed by a video of the incident, would clear their record signing.
They were given reason for optimism on Friday when the FA's video advisory panel agreed there were grounds for appeal and passed it to the disciplinary board at Soho Square for consideration, who yesterday ruled against Roberts.
He now misses Saturday's home game with Crewe, the visit to Bradford, and the clash with former club West Brom who sold him for £1.4m in January.
Manager Paul Jewell was given the news as the squad was travelling to Kent ahead of tonight's game with Gillingham.
He said: "It's a disappointment but we have to get on with it, and this will give someone else their chance."
Roberts got a straight red card from referee Phil Prosser in the second half at Stoke for kicking out at full-back John Halls.
Latics immediately put forward their appeal, with video footage of the incident appearing to show that the striker was only trying to get his foot untangled from Halls' boot.
But the decision means Roberts signs off from first team duty after tonight's game for more than a fortnight.
He won't be available again until Coventry visit the JJB on March 20.
Of more immediate concern is the clash at Gillingham, and Latics could move into the automatic promotion places if they pull off their first win in Kent for almost a decade and West Brom lose at leaders Norwich, a clash being shown live by Sky Sports tonight.
Jewell, though, is just concentrating on his own side's result, and he is expecting a tough test against Andy Hessenthaler's men.
Jewell said: "It's a difficult place to go and I've never had a result there so I'm due one.
"Gillingham are a bit like Walsall who we played on Saturday, in that they're a side who no-one really enjoys playing against.
"They have a super manager who is also arguably one of their best players.
"It's a tight ground, but we're looking forward to playing on a decent surface and trying to keep our run going.
"We're up in a good position and I don't want us to be a team which falls at the final few hurdles.
"There are only five points between eighth place and third at the moment, so we're not resting on our laurels."
Jewell is disappointed that the longest away journey of the season has fallen in midweek.
The squad set off for the south-east after lunch yesterday, and were expected to fit in a short training session this morning, Jewell said: "It's a long way to go and I feel sorry for the supporters.
"We had the luxury of stopping overnight in a hotel, but it's different for the fans.
"It's crazy that we should be playing this game on a Tuesday night."
Latics left Steve McMillan behind after the full-back picked up yet another injury.
He hurt his groin muscle while doing a warm down after Saturday's win over Walsall, a game in which he was an unused substitute.
His place on the bench is expected to be taken by either Neil Roberts or Mike Flynn.
Skipper Jason de Vos is another slight doubt after taking a knock at the weekend, but should be passed fit.
Source: Wigan Evening Post.