Ben Watson scored the only goal of the game with a looping 82nd minute volley after the home side had dominated the game for large periods.
The result rekindles the Lactics' ambitions of qualifying for the UEFA Europa League next season, while the Tigers look nervously over their shoulders as they stay four points clear of the relegation zone.
And the City boss accepted that his side were second best on the day, Brown said: "The first half I don't think we played particularly well.
"Second half we came out of the traps a little bit better, a caused one or two problems but consequently they have got a winning goal and for me the difference between the two teams is the experience for Wigan at this level and we've got to learn from that."
Hull lost defenders Andy Dawson and Kamil Zayatte through injury but the Hull manager refused to accept losing the pair was the reason for defeat.
When asked if it made a difference Brown added: "Yes, but we are not excuse-makers."