"I'm having a moan at my players for the last ten seconds of a game which we have totally dominated," he said.
"And we have lost four points against two of the three top teams."
Striker Bothroyd added: "We are letting in silly goals and we have get better than that otherwise we won't win the promotion that we believe we can achieve.
"When we play Wolves, Birmingham or Reading we want to go there and win because we think we are a better team than them - and we have shown we are better because we dominate the games for large amounts.
"We impose ourselves and still feel we can win automatic promotion because all you need is a good run of victories."
Cardiff, now unbeaten in nine league games, left St Andrew's feeling as if they had lost but captain Joe Ledley tried to put some perspective on the result.
"Before the game we would have taken a point from Birmingham away," said the Wales midfielder.
"But if you look at the game, we should have won and now it feels like a loss for us.
"It has happened too many times this season and when you're in play-off contention a draw is not enough, we need to win these kind of games.
"We have proved we can live with the best in the division and we defended well but we lost it in the last seconds."
Jones, though, was adamant Bowyer's last-gasp lever should never have stood after the the visitors twice failed to clear in the area.
Video replays suggested defender Radhi Jaidi had fouled Roger Johnson as Cardiff failed to clear their lines, and Jones could not believe referee Michael Jones failed to give it.
He said: "I think if the referee looks at it again, he's given all of those pushes and fouls all day and the one time that we want him to give one - he hasn't.
Cardiff wingers Peter Whittingham and Paul Parry were replaced with knocks at St Andrew's but both are expected to be fit for next Sunday's FA Cup fourth round glamour tie with Premier League giants Arsenal.