Marouane Chamakh had given Palace the lead just after the half-hour mark but a quick-fire double from Stoke in the second half was enough to give the hosts victory.
However, Holloway expressed only disappointment for his players after a decent showing in the Potteries.
"I feel disappointed for them," he told Sky Sports. "I think we had a little crazy spell in the second half where you know they're going to have a go at you.
"Mark (Hughes) had the half-time team talk to get at them a little bit so we just had to weather that spell and, unfortunately, we didn't.
"(They scored) two goals in quick succession from throw-ins which we weren't quite right positionally and one or two of my players were tiring because they haven't had a proper pre-season, in particular with us.
"That's life, you've got to get on with it. We've scored our first goal, we haven't got our first point yet but I'm very, very encouraged with that to be honest."
The former Blackpool boss was pleased with the impact of Chamakh after the Moroccan netted on his full debut for the Eagles and hopes he can bring in more new players before the transfer window closes on 2nd September.
"I wouldn't say (we were in) control, we're finding our feet at this level. It just goes to show not every goal is a pretty goal in this division," he added.
"Marouane wanted to get there, didn't he? We cleared it down the line, their crowd were going 'woof'- which is quite embarrassing.
"Marouane wanted it, he got on it and it was a great finish. It gave us a platform but unfortunately we couldn't see it through and I've got a bit of work to do this week to try and get some players in to help the boys I've got.
"(I'm) completely delighted with the way they set about it and I feel disappointed for them but that's the Premier League."