108 mins
The Clydesdale Bank Premier League side dominated possession throughout against their Ayrshire rivals but were thwarted by goalkeeper Kevin Cuthbert who made great saves in the second half from Gary Harkins, Shiels, Manuel Pascali and Garry Hay.
However, Cuthbert's resistance was broken in the 109th minute when Shiels drove low into the corner to set up a final appearance against either Celtic or Falkirk, who play in the second semi-final at the national stadium tomorrow.
Kenny Shiels made two changes for Kilmarnock's Scottish Communities League Cup semi-final against Ayrshire rivals Ayr United at Hampden.
Central defenders Mohamadou Sissoko and Zdenek Kroca dropped out, the latter starting on the bench, replaced by debutant Michael Nelson and midfielder James Dayton, with skipper Manuel Pascali moving back into defence.
Killie midfielder Dean Shiels shrugged off an illness to keep his place while, for the Irn-Bru First Division side, midfielder Alan Trouten returned following a hamstring injury and striker Gareth Wardlaw came back in, with Mark Roberts and Adam Dodd on the bench.
Ayr's part-timers had the scalps of three Clydesdale Bank Premier League sides - Inverness, Hearts and St Mirren - already under their belt as they got the game under way, following a false start.
Hampden appeared around half-full but there was a decent atmosphere and the fans watched Killie make the more positive start.
The Rugby Park men had the first effort on goal in the sixth minute with Shiels sending an unconvincing drive from 25 yards wide of the target.
Ayr's lone striker Wardlaw was seeing little of the ball as Kilmarnock, bolder, sharper and more purposeful, took control and began racking up the corners but Somerset Park keeper Kevin Cuthbert had yet to be fully tested.
Killie began to turn the screw with Ayr captain John Robertson having to head a chip from Killie midfielder Garry Hay off the line at the expense of another corner, which came to nothing.
The SPL side strengthened their grip on the game and in the 26th minute Hay ended another spell of pressure with an effort from distance which Cuthbert clutched to his chest.
Ayr's first effort on goal came in the 33rd minute when wide man Michael McGowan sent a free-kick from 25 yards curling over the Killie bar, before Shiels again drove wide at the other end.
In the 38th minute Cuthbert made a close-range save from Ben Gordon after the Killie defender had raced into the Ayr box to confirm the feeling the first half was destined to remain goalless.
Killie forced another corner within a minute of the restart after Gordon ended another fine over-lapping run into the box with his cut-back blocked but again it came to nothing.
Five minutes later on the other wing, Dayton went past Ayr defender Eddie Malone and burrowed his way into the United box but could not pick out a team-mate and another opportunity was lost.
As Killie pressed again, striker Paul Heffernan's shot from the edge of the box was deflected by Trouten for another fruitless corner, which brought the first groans of frustration from the Killie fans.
In the 55th minute the increasingly influential Shiels drove at the Ayr defence before laying the ball off for Gordon but his side-footed effort from the edge of the box was easily gathered by Cuthbert, who made another save from Hay's long-distance effort moments later.
On the hour mark Roberts replaced the tiring Wardlaw but the traffic continued towards the Ayr goal.
In the 66th minute he parried Dayton's 25-yard drive to the feet of Gary Harkins and stuck his leg out to deny the Killie striker's close-range strike which looked certain to give the Rugby Park side the breakthrough.
In the 79th minute Cuthbert stretched to tip Shiels' 30-yard drive over the bar and from the corner knocked Pascali's downward header past for another corner which Ayr survived.
Killie keeper Cammy Bell made his first save of the game in the 82nd minute from Andy Geggan's drive before Cuthbert tipped Hay's powerful drive over the bar for yet another corner which Killie squandered as the game headed towards extra time.
In the second minute of extra time Killie substitute David Silva, on earlier for Dayton, screwed an angled drive wide of the far post.
Penalties were on the cards but in the 109th minute Shiels eventually got the breakthrough against a desperately unlucky Cuthbert.
The Northern Irishman's first drive was parried by the former St Johnstone keeper, who then saved from Heffernan but when the ball came out again Shiels rifled it low into the net.
Finally, Ayr responded, throwing everything forward but Killie held out for a deserved victory.
Post Match
With scant disregard for the protocol of the occasion, Kenny Shiels accused Ayr of being intent on reducing the game to a penalty competition, of parking the bus and not showing any ambition to win the match in normal time. A body of evidence that included just one shot on target during the 120 minutes suggests the Rugby Park manager to be entirely correct....
"Football is about two teams going out to win a game, Today there was only one team trying to do that. I'm delighted for the players because they stuck at it and were patient. It was thoroughly deserved, It was a fantastic performance. They came for penalties and almost got there. Football is a game that should be played with expression and we showed great courage, we attacked for the whole game. When they come out they look as if they can play. I wish they had done that more. If they had come out, it would have been a better game. The Ayr players deserve so much credit for their work rate and how much they put into it. But I think if they had come out they could have won the match and maybe that's a lesson for them. Destiny is a wonderful thing, I was thinking for the whole of the second half that there was something going on with the man upstairs and that they were going to score. It's happened to me before and I thought Ayr were going to go through because we weren't getting any breaks."
On referee Steven McLean... "James Dayton, the most influential player on the pitch, was kicked from pillar to post, I said to the referee 'would you please give him some protection' and what did he do? He went and booked him. What's that all about?
"Football was the winner today and I'm so pleased for the chairman and the supporters."
Losing manager Brian Reid said... "Kenny should keep his opinion to himself, he should worry about his own team,"
