A brilliant Charlie Adam winner secured a vital three points for the Potters in their fight for survival, but the result was down to a collective team effort as United threw everything at them late on.
And Hughes could not hide his pride after his side held on for the win, which was Stoke's first in the league over United since Boxing Day 1984.
"The seven minutes of extra time at the end were a bit of an ordeal, but credit to the lads who were absolutely magnificent," Hughes said.
"We got a little bit of luck, but you need that sometimes, and it is something we feel we haven't had in recent months.
"But right through the course of the game I thought every one of them gave their heart and soul into what we were trying to do today, and we got our just rewards for once."
Adam's second of the game came just after United had got back on level terms, and looked set to go on and net all three points.
But Hughes admits the thunderbolt did not surprise him, as he has seen it all before.
"We are getting to the point where we are not surprised by Charlie," Hughes added.
"Wherever the ball drops to him outside the area you know he is going to get a shot at goal.
"The winning goal was such a great strike, and the keeper was never going to get anywhere near it.
"Today we got our reward from a huge amount of effort, not just today, but over the last few weeks."