Bowyer’s men were just five minutes from securing a vital three points on the road courtesy of Michael Cain’s late free-kick.
But a controversial and mysterious penalty handed the home side a route back into the game, when former Stanley player Tom Aldred was adjudged to have fouled Romuald Boco.
Boco tucked it away, then went on to inflict a heart-breaking defeat on the Seasiders with a winner in the final minute of injury time.
Bowyer was incensed by the penalty award, after the officials had wrongly ruled Kyle Vassell’s close-range effort offside while the scores were still level.
The Pool boss said: “The linesman – who, let’s say, was being intimidated all afternoon – disallows a goal for offside. I’ve seen it again –it’s not offside.
“But we do well, we keep going and we score a good goal. I don’t think anyone in the building sees the penalty decision and I don’t think anyone in Accrington sees it.
“If anything it’s a foul on Tom Aldred as he goes to defend at the front post.
“But there’s no excuse for their winner. That was poor from us and they’ve been told that. In the last 30 or 45 seconds of the game, not to track back is unacceptable.”
Bowyer said his concerns over officiating were far from a one-off. “I’ve spoken to him (referee Andy Haines) but that’s only for my benefit. It doesn’t help us,” he added.
“It’s just incredible how they get it wrong so often. It’s not just me, it’s every manager you speak to. I bet on Saturday night you see 15 others saying the same thing and that’s just not acceptable.
“Two big decisions – the offside call and the penalty –it’s unfair on everyone connected with football. Supporters pay money, and our fantastic following have been badly let down.”
The match had been a tight and nervy affair, with little quality on show from either side. Bowyer was frustrated to see his side fail to hold on to a lead and secure what would have been a second win in eight games.
He said: “Their goalie makes a great save from Brad Potts when we were 1-0 up, so we had a chance to eliminate the errors of the officials but we’ve not taken that.
“I thought we were comfortable but the penalty has given Accrington a lift, which they didn’t really have before, and it gave them that belief.
“It was a nothing first half – both teams just cancelled each other out. I thought we started to gain control in the second half but it’s amazingly frustrating at this moment.
“The fans were fantastic. I feel gutted for them.”