Reda Johnson's first-half header gave Wednesday a deserved lead, but Robert Koren equalised for off-colour Hull with seven minutes remaining.
However, Hull goalkeeper Eldin Jakupovic dropped Miguel Llera's corner into his own net three minutes later, and deep into stoppage time Michail Antonio raced clear to clinch a 3-1 win, although the home side still had time to miss a penalty through Jay Simpson.
"We've got good young players and we worked our socks off today," Jones said. "We frustrated them and they had nowhere to go.
"We didn't come here with a defensive line-up. When we had the ball we needed to use it, and we did.
"Sometimes when you have a big man up front you go long a lot, and we knew we couldn't do that today. But we had a quick team.
"The unit was really solid. We know there's a long way to go, but we've been playing well. We just have to take our away form into our home form."
Both managers were perplexed by the performance of referee Mark Haywood, with Jones particularly unhappy with the decision to disallow a strike from Giles Coke early in the second half.
"We would have felt hard done by if we hadn't come away with a win," Jones said. "At 1-0 we scored a perfectly good goal and for the life of me I can't understand why he's disallowed it.
"You have to give the linesman credit for our second goal because the ball did go over the line. At least the linesman stood strong because I don't think the referee was going to give it. If we hadn't have got the three points I would have been here berating the referee."