Chris Basham’s 43rd-minute sending-off proved influential to the result as the Blades went down to goals from Ben Williamson and Dany N’Guessan.
Basham was shown a straight red card for a challenge on former Blade Michael Brown as the Valiants claimed their first home win over their opponents for 31 years.
“It was never a sending-off; it’s unfortunate because it altered the course of the game,” reflected Clough.
“Their manager Rob Page came over straight away and said it was never a sending-off, but we should have taken more of our chances.
“The officials have made some decisions which have unfortunately affected the result. We made one or two poor decisions, but we still deserved to get something out of the game with the chances we created.
“It’s frustrating because we’d got back in the game and then a silly challenge to concede the penalty has cost us.
“For 20 minutes after half-time we looked the better side even though we had 10 men.
“But it’s a bitter blow Chris is suspended for three games now and we’ve lost the game.”
Midfielder Jamal Campbell-Ryce had cancelled out Williamson’s early opener, but N’Guessan’s 79th minute penalty saw any hopes of a point disappear.
Port Vale: Neal, Yates, Dickinson, Duffy, Dodds (Lines 75), Williamson, O’Connor, Brown, Marshall, Veseli, N’Guessan (Daniel 85). Unused substitutes: Johnson, Robertson, Birchall, Nimely, Campion.
Sheffield United: Howard, Harris, Basham, Doyle, Murphy, Scougall (Reed 71), McGahey (McNulty 84), McEveley, Campbell-Ryce, O’Grady, Cuvelier (McCarthy 45). Unused substitutes: Baxter, Higdon, Turner, Adams.
Referee: S Atwell (Warwickshire)
Man of the match: Jamal Campbell-Ryce.