Angry scenes broke out after referee Harry Hawkins had awarded Welfare a second penalty of the night as Joel Freeston had been fouled in the 93rd minute of a frantic match.
The Maltby players were incensed by the decision and most of them surrounded the referee and it resulted in Ashley Linacre being shown a red card for dissent.
After a two minute delay, Ward stepped up to slam the penalty home and a delighted Welfare manager Rob Hunter said: “It was a tough game because when you come to places like Maltby, it’s not a great pitch and it has a big slope on it and the bounce of the ball was terrible.
“Both teams cancelled it each other out because both teams played 4-3-3.
“It was even-stevens and there was nothing in the game. We probably edged it slightly in the first half on chances. Kieron missed a great opportunity at 0-0 and we had a couple more. In the second half for the first 20 minutes they were the better side and they had two chances that flashed across the six-yard box.
“But we have shown great character as we kept going forward and just before the penalty, Paul Hagreen who has been outstanding again tonight put a quick clearance forward and it has put Joel Freeston through. He just thumped it on the volley and it went just wide.
“Two minutes later Joel has shown great determination to get the header in front of the defender and he has got dragged back. It probably was a bit harsh, but the kid did definitely drag him back.
“Calum finished two great penalties tonight and when it was given Joel grabbed the ball. He wanted to take it, but I thought because Calum put the first one away so well and that’s he’s on fire at the moment, he should take it.
“There was a lot of pressure on him and he just said to me that he felt physically sick taking the second penalty. He was very nervous, but he has put it away really well. He has now scored in five consecutive games.”
Maltby scented blood and Hagreen then kept Glasshoughton in the game with a fine save from Maltby player-manager Brian Cusworth.
Glasshoughton responded on the half-hour mark. Striker Ward was fouled and Glasshoughton’s leading goalscorer sent Maltby goalkeeper Jamie Bailey the wrong way to level the scores.
The game was being played at a fast pace, but with Maltby creating more chances. Black and Branagan were causing the most problems. Hagreen had to deny Black before the winger was replaced by Matthew Bradley.
Glasshoughton looked nervy at the back and passes were going astray. One poor pass led to Branagan rounding Hagreen. Fortunately he could only find the side-netting.
But, there was still time, deep into injury-time. Referee Hawkins adjudged that Freeston was uphended, sparking ugly scenes. Linacre was given a straight red card and Branagan was yellow carded for their part in the protests.
Welfare still had to survive two more minutes before Hawkins was again confronted at the final whistle by angry Maltby players and officials in scenes which are likely to be investigated by the FA.
Glasshoughton, who celebrated a last gasp 2-1 victory at Maltby for the third consecutive season, visit Askern Villa in the FA Vase on Saturday.
Glasshoughton Welfare: Hagreen, Beaston, D Ward (Clayton 67), Tuck, Chappell, Low, Middleton, Young (Freeston 37), Pell, C Ward, Corley (Hirst 57). Subs unused: Edwards, Halpen.
Referee: H Hawkins
Man of the match: Paul Hagreen (Glasshoughton Welfare)