Twice Wigan came from behind but theyhad the chances to win this one and were denied when Begovic acrobatically tipped a Charles N'Zogbia effort on to the post in the 83rd minute.
'You're looking at an experienced and strong Stoke side and when you give them the lead, the games become very difficult,' said Wigan manager Roberto Martinez.
Close up: Wigan's Charles N'Zogbia sees his shot hit the post after the save from Stoke goalkeeper Asmir Begovic
'They got a deflection for the first goal but we never folded, we reacted in the right manner and it took an outstanding save at the end to prevent Charles scoring.'
Unbeaten in the previous four matches, Stoke claimed a fortunate opener with Robert Huth's 25-yard free-kick deflecting off the wall and sending goalkeeper Ali Al Habsi the wrong way as it trickled into the opposite corner.
Boiling point: Tempers flare between Wigan and Stoke players
MATCH FACTSWIGAN (4-5-1): Al Habsi; Gohouri, Alcaraz, S Caldwell, Figueroa (Stam 73min); N'Zogbia, Thomas, Diame,Watson, Cleverley; Boselli. Subs (not used): Pollitt, Gomez, McArthur, Boyce, McManaman, Mustoe. Booked: Figueroa.STOKE (4-4-2): Begovic; Huth, Shawcross, Collins, Higginbotham; Walters (Whelan 70), Delap, Whitehead, Etherington; Fuller (Tuncay 83), Jones. Subs (not used): Sorensen, Gudjohnsen, Diao, Faye, Shotton. Booked: Begovic, Shawcross, Fuller, Walters.Referee: M Jones (Cheshire).
Wigan's equaliser after 30 minutes was just as lucky, James Collins putting Ben Watson's free-kick past Begovic.
Stoke regained the lead a minute later through Matthew Etherington, who fired home Ricardo Fuller's cross.
Hendry Thomas missed a sitter but TomCleverley made amends five minutes before half-time when his deflected shot beat Begovic.
Stoke are now seventh in the table but manager Tony Pulis would only say: 'We had a three-year plan when wegot promoted and we said we needed to be in the Premier League for three years for the club to push on. Nothing has changed.'
High jump: Wigan's Tom Cleverley celebrates scoring an equaliser
Liverpool eye Stoke's Shawcross but Agger warns he won't be forced outWigan boss Martinez considers his options after Moses blowSTOKE CITY FC