The Latics chairman says the 37-year-old is free to join Villa if he likes, but is confident of hanging on to his man and has offered the Spaniard a new and improved contract to encourage him to stay.
"I had a good meeting with Roberto and the decision whether he is going to stay or go is entirely in his hands," Whelan told BBC Radio 5 Live.
"I will support him whichever way he wants to go.
"I've offered him an extension to his contract and a better contract, because his current deal is down to a year.
"I have asked him to make a decision and tell me and the rest of the world, and I think he will be doing that in the next 24 hours.
"My gut feeling is he will stay at Wigan, but he will move in 12 or 18 months or two years, and he will go to one of the top European clubs."