The visitors equalised in the 59th minute after a brilliant piece of skill by Nahki Wells, who fired in the loose ball from two yards after his initial effort was saved.
But Vale's winner arrived seven minutes later when Doug Loft struck a deflected 20-yard shot from Hughes' perfect lay-off.
Parkinson said: "It was a full-on competitive game and I thought over the 90 minutes we had the better chances and deserved something out of it.
"We knew Vale would be fired up after a defeat last week and I warned my players exactly what sort of game it would be.
"We didn't handle that too well in the first-half when Vale were better than us in certain areas. We didn't stop the crosses coming into our box well enough and were put under pressure.
"James Meredith has been brilliant since he joined us, but the pitch was sticky and not the kind of day to pass the ball back to the 'keeper.
"But we got the reaction we asked of our players in the second-half. We defended much better and managed to get back on terms before losing to a very disappointing goal.
"The lad (Loft) struck the ball well, but Jon McLaughlin would have saved it comfortably if it hadn't taken a big deflection. It's one of those things and we have to move on to next week and make sure we play for the full 90 minutes."