The Villa boss felt his side never recovered from going a goal behind.
The Latics grabbed all three points with a goal in each half as they claimed a first win under new manager Roberto Martinez.
Striker Hugo Rodallega bagged the first goal with a sensational strike in the first half before Jason Koumas doubled their lead after the break.
Speaking after the game O’Neill admitted he was pleased with the way his side had started the game but insisted they had struggled after going behind.
“We started pretty well and when Wigan scored it knocked us back more than it should have done,” the Villa boss told BBC Sport.
“I thought Wigan played very well.
“We are a lot better than that - we know that and have to do something about it.”
The result is Wigan’s first ever Premier League opening day win but leaves Villa with much thinking to do ahead of their next game against West Ham United at Upton Park.
Gill Clark, Goal.com