Speaking to the Wigan Evening Post, Whelan said: "We can't rest easy, but I am confident now that we will survive.
"That win virtually makes us safe, and it is so important for the club that we get there. When we came up, everyone told us to enjoy our one year before we went back down.
"Next year would be our sixth year, which is wonderful for a town like Wigan. The longer you are in the Premier League, the better you get and the more you can grow as a club.
"We are not the biggest or the best supported club in the division, but what we do have is loyal supporters. And when we play like we did on Sunday, it is just remarkable."
The chairman was particularly impressed with the final ten minutes and admits that he didn't see a way back from 2-0 down.
"I thought with 10 minutes that if we could get a goal then 2-1 would be a respectable score," he added.
"We'd had a blatant penalty – the biggest, blatant penalty I have ever seen in my life – refused, and I thought that we deserved at least to make it respectable.
"When we got it back to 2-2, I think we were all happy with that. We'd have taken a point. But to then get the winner – that was just unthinkable and unbelievable.
"I am so delighted for the lads, and they deserve every bit of praise they get. We have struggled a little bit this season, with certain players in certain positions, but it was just a wonderful day for Wigan Athletic.
"And you will never get a better end to a game than that. Never, ever."