The Paraguyuan international defender was making his season debut after returning late to pre season from the Copa America.
The toll of a busy season and summer have taken their toll on the body of Alcaraz who has now suffered a bad injury.
Speaking about the injury, Latics boss Roberto Martinez told the Wigan Evening Post: "We're hoping he'll only be out for six or seven weeks, but the worst-case scenario is two months, maybe even three.
"You have to be very, very careful when it comes to soft-tissue injuries, because if you come back too early you are risking further damage, it is a major, major blow for us and we are going to miss Antolin badly over the next few weeks.
"On the plus side, Antolin is a very fit boy with a very strong character, which gives you hope he'll be back sooner rather than later but it is a major, major blow for us.
"All we can do now is help Antolin to recover fully and make sure he is back fit and raring to go for the remaining two-thirds of the season."
The Latics are now set to be short at the back with Steve Gohouri also out with a calf injury. Emmerson Boyce is set ot deputise at centre back with Ronnie Stam coming in at full back.
