Jones had five key players out - including strikers Craig Bellamy, Jay Bothroyd and Michael Chopra plus midfilders Seyi Olofinjana and Danny Drinkwater - and could be short of numbers again at Ipswich on Saturday.
He said: "We got ourselves into a winning position and the frustrating thing is we had spoken about the boy King breaking into the box.
"Maybe it was a bit of fatigue but we got caught out. They were the better team in the second half so I can't complain.
"We passed it well in the first half but we stopped doing that and maybe you can put that down to fitness from players who haven't had a pre-season.
"We were always worried about our fitness tonight and two games in three days was a step too far at the moment.
"We don't know if they will be fit for Ipswich yet. We had five big players out and we were stretched. It's unusual but hopefully we can get one or two back and go again.
"If I had those players available it makes a big difference and we couldn't change the game when we went behind."
Jones was also quick to dismiss any claims Naylor may have had for intending his long-rang strike.
Jones said: "He's crossed it.
"He knows he's crossed it and it's a lucky goal but we had a few chances in the first half."
Paulo Sousa was pleased to see his side grasp the nettle and go out and win the game after being a goal down at half time.
Sousa said: "I am very happy and we have deserved this win before so it is nice to get under way. I feel the team is closer to my personality now.
"We had the character, anger and desire to win the game and my image is on them now.
"I recognised the anxiety in the stadium when we went behind but we had been playing well.
"We finished the first half well and we raised the intensity after the break.
"We increased the tempo and had much better quality in our movement. We created good chances and controlled the game. But I knew it was coming.
"During the international break the players' approach changed. They started to understand what approach we needed and the spirit and attitude.
"We were much more positive in everything we do and we need to be consistent now."