The Potters trailed Southampton 2-0 at the break in their fourth-round tie at the Britannia Stadium last night, before eventually recovering to level the game up.
However, Stoke collapsed in the closing minutes when Graziano Pelle struck just moments after Peter Crouch was dismissed for a second yellow card offence, ensuring that Hughes's charges tasted defeat.
"We put in a huge effort in the second half," BT Sport quotes the Welshman as saying. "We needed to because in the first half we didn't really get anywhere near the intensity that I was hoping for in terms of making it a real cup tie.
"The difference with the second half was marked. It was a real effort and I thought the momentum was with us. At 2-2 I felt we were in the ascendancy and we could go on and possibly win it from a situation where at 2-0 down you think it's going to be very hard against a very good Southampton team."
Stoke return to Premier League action on the weekend when they host West Ham United.