The Blues needed some reward from White Hart Lane for their Europa League ambitions but Hughes was furious when Halsey pointed to the spot after Fraizer Campbell went down under a Micah Richards challenge.
The on-loan Manchester United striker had come off the bench with 15 minutes to go and skipper Richard Dunne led angry protests about the penalty before Robbie Keane sent Shay Given the wrong way from the spot.
Spurs boss Harry Redknapp claimed Richards “was all over him and dragged him down”, but City’s boss said: “The ref has made a really poor decision that has cost us the game and it’s really disappointing. There have been games this season where we’ve not deserved to get anything, but that wasn’t the case today.
“I’ve no idea why he’s given it. It was a speculative ball into Shay Given’s hands, never a clear-cut goalscoring opportunity. Maybe the angle the referee had made him appear closer to the ball than he was.
“That’s the only excuse I can give him, because fundamentally that’s a very poor decision. I banged on the ref’s door as I went past! But I don’t think there’s any point trying to speak to him about it.”
The Blues’ bid for seventh place and a Europa Cup spot next season was immediately ended simply by rivals Tottenham’s victory, but Fulham’s win at Newcastle left Roy Hodgson’s team in the driving seat.
City thought they had rescued at least a point when Valeri Bojinov snapped up a superb 65th-minute equaliser to cancel out Jermain Defoe’s 28th-minute opener, only for Keane to despatch that late winner.
Hughes said: “We would have loved to be back in Europe and that’s obviously not going to be the case now.
“We were much better in the second half. First half we were tentative and allowed Spurs to dictate, so they had the momentum, but after the break we were a lot more positive and got back to 1-1.
“We were all pleased for Boji, it was important that he got back on the goalscoring trail and everbody saw what it meant to him. With three minutes to go, we felt we were the team most likely to score.”
