Until the final stages, things went very much to the script for Premier League side Wigan, who took a two-goal lead through Mohamed Diame and a first for the club from 19-year-old striker Callum McManaman.
A late double from Hull veteran Nick Barmby kept the hosts in contention, but Diame's second 13 minutes from time ensured it was the visitors who emerged victorious.
Pearson said: "If I'm honest, the scoreline at the end makes it look a little bit closer than it was. I think we were undone with a bit of pace and power and athleticism and they were by far the better side.
"I was disappointed we didn't get among them a little bit more and put them under more pressure. We talked about the tempo of that game before the start and we just didn't get about the field.
"We finished the game pretty well, but we were also very open at the back."