Bottom-of-the-table Pools ended a 22-game winless run to become the first team to win at Bramall Lane in the league this campaign.
Two headed goals from veteran striker Steve Howard helped Hartlepool on their way to a surprise 3-2 success, with Sheffield Wednesday fan Ritchie Humphreys also on target for Pools.
Michael Doyle equalised to send the teams into half-time all square at 1-1 and Harry Maguire netted in stoppage time for the Blades.
Hughes heaped praise on his players after seeing them win for the first time since he took charge last month.
He said: "I think the heavy pitch suited us because it slowed it down. Take nothing away from the guys though for their effort and commitment though, to come away to the league leaders and score three goals is fantastic.
"Hopefully that will give us the confidence and the momentum to go and try and build on that.
"I'm delighted for the players. We knew they would have a right go at us in the second half so I said to the boys that they had to go and match it, and they won their one-on-one battles.
"We scored the goals at the right time. There are some wonderful people at the club who've supported me since I've joined Hartlepool and that victory was for these guys.
"Hopefully now we might see one or two of the players coming to training with a spring in their step and not feeling sorry for themselves. They've set a benchmark by beating the leaders away from home."