The Trotters knew only victory at the Britannia Stadium, coupled with defeat for QPR at Manchester City, would be good enough to keep them in the top flight.
Things were going Bolton's way at half-time, with bizarre goals from Mark Davies and Kevin Davies cancelling out a controversial opener from Jon Walters, while City were also ahead.
But QPR came back to lead and, even worse, Walters equalised from the penalty spot, while City's dramatic turnaround meant Bolton's fate was only back in their own hands when the final whistle had blown in Stoke and it was already too late.
Coyle reserved much of his anger for referee Chris Foy, who allowed Walters' 13th-minute opener to stand despite the striker appearing to head the ball out of Adam Bogdan's hands, and the Bolton boss also felt the goalkeeper should not have been penalised for felling Crouch to concede the penalty 13 minutes from time.
"It's hard to take," said Coyle. "We had a slow start in the game but I think the events that happened today, and I know people will talk about sour grapes, but how can that first goal be allowed to stand when Adam Bogdan had clearly got the ball in his hands?
"Jonathan Walters is a good player but he sticks his head and his elbow halfway up Adam's arm, I find it incredible. I've been in to see the officials - I've done that a lot this season and I can't say you come out any the wiser.
"But we bounced back, got 2-1 in front, had chances to make it 3-1. Crouch has a great chance and Adam makes a great save, but in the aftermath Crouch has knocked it by Adam and it's actually Crouch who's clambered into Adam.
"I don't think we've come out on top of the decisions today [Sunday], but we've picked ourselves up again. Lee Chung-yong had a good chance to get that third goal and then Tim Ream's header in the last minute, where the keeper's made a great save.
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"And that's the margins in this league. If that goes in, we're still in the Premier League."
It was a cruel end to the most difficult of seasons for Bolton, who have been beset by long-term injuries to key players and also had to deal with the trauma of Fabrice Muamba's on-pitch cardiac arrest.
The midfielder's remarkable recovery will certainly put relegation into some perspective, and Coyle has no doubt the Trotters will get over the disappointment ahead of next season.
The Scot said: "There's nothing that takes away from the disappointment and everything that will come with that.
"We'll take our medicine, I will as a manager, but we certainly believe, regardless of the personnel we had missing and the trials and tribulations of the season, that we still had enough quality, and we do.
"Our young players will continue to get better, that's the transition we've been making this year, but we wanted to do that off the platform of being in the Barclays Premier League.
"My feelings are not for me, they're for our wonderful support and the chairman and the owner. It's a wonderful club.
"The players are very quiet and sombre, it's not a feeling I've become accustomed to as a manager but it's happened and it's about how you react to adversity. We will regroup and we'll look to bounce back straight away."
Stoke certainly played their part in shaping the relegation battle after losing to QPR last week, and boss Tony Pulis admitted the nature of Bolton's goals left him thinking they would stay up.
In the 40th minute, Robert Huth's clearance smashed against Mark Davies and flew into the net, then five minutes later Kevin Davies' mis-hit cross caught out Thomas Sorensen at his near post.
Pulis said: "We have a responsibility as a football club, and I think we did at QPR last week, to do the best we possibly can. Irrespective of whether you're playing against friends or whether you've got a soft spot for a team, you have to do your best.
"And I thought in the first 20 or 25 minutes we were really on top. I have to say I came in the dressing room at half-time and I thought it was going to be Bolton's day. They were two bizarre goals.
"But we kept at it second half and the draw wasn't good enough for Bolton. I'm disappointed for Owen and Bolton but it's a reminder to everybody in this league that you have to keep pushing on because it's such a tough league."