"I'm sure Villa will be disappointed," Whelan told Sky Sports News.
"I'm over the moon and I'm sure every Wigan supporter will join me in saying we're so pleased we've got Roberto.
"I don't think we were really close to losing him but he has to consider his future. He's going places, we all know that, and Aston Villa are a big club. When you get a club like Aston Villa wanting your services it's something to be proud of.
"I think Wigan people will look at this and think 'Roberto is showing that football is not greed and everything that people believe it is'," added the Latics chief.
"Football is a sport with loyalty in it and he's been so loyal to me over this that we should look at that. The Wigan people, the supporters, go and buy your season tickets - that's all I can ask them to do.
"We've had a quick word about that (next season) and Roberto's intentions are to finish in the top 10."