Glenn Murray took the tie to extra time thanks to his 87th-minute penalty which cancelled out an earlier effort from Kenwyne Jones.
Jon Walters sealed the hosts' win with two goals before substitute Cameron Jerome wrapped up the victory, leaving Holloway to reflect on the success of the Barclays Premier League side.
He said: "I think Tony has done a fantastic job. I think his team are honest, hard-working and never stop, and Jon Walters just sums all that up for me.
"You see what he did on Saturday, but you wouldn't have known he ever dreamed of making a mistake. He is a wonderful fella, a brilliant player and a credit to Stoke.
"I feel a little bit aggrieved because my lads didn't deserve that overall (to lose 4-1). But that is where they (Stoke) are and where we are trying to get to, and for now I'd rather take all the positives out of it."