Cole Skuse had put the Robins ahead before the visitors were rewarded for their attacking approach when Boyd marked his 124th consecutive appearance with a header home in the last minute of normal time.
The equaliser denied the hosts a place in the top six but Ferguson was adamant his team deserved at least a point and might well have taken all three.
"I'm disappointed and frustrated because I feel it was another game we should have won." said Ferguson.
"We got a lucky break with our goal at the end, but had some great chances before that.
"If Craig Mackail-Smith had taken his early opportunity it would have been a totally different match. No opponents like chasing games against us because of our pace on the break.
"Bristol is a difficult place to visit and we would have taken 1-1 before the game. Their home record is very strong so it is a good result for us in a way."
Boyd had his back to goal on the edge of the box when he headed on Danny Rose's last-minute cross from the right. The ball sailed over City keeper Dean Gerken and in off the far post.
"It wasn't even a chance," said City boss Gary Johnson. "But I
never felt we were home and dry because one goal is never enough.
"Peterborough probably deserved a point the way the game went and we now have to beat Plymouth here on Tuesday night to get ourselves into the top six."
Midfielder Skuse had put City ahead with a fine solo effort on the half-hour, taking on one defender and bursting between two more before scoring with a low shot from 12 yards.
Skuse hobbled off seven minutes from time after a fine individual contribution, but Johnson said: "We don't think the injury is serious and hopefully Cole will be okay to face Plymouth.
"We have been trying to encourage him to be more penetrating and you can't be more penetrating than he was with his goal. He was a forward-thinking player today and that's what we want from him."
Both goalkeepers excelled in a tight contest. Gerken did brilliantly to beat away Mackail-Smith's eighth- minute shot after the striker had broken clear on to Boyd's pass.
On 58 minutes Mackail-Smith was denied again as Gerken produced an even better reaction stop to keep out his close-range volley.
Peterborough keeper Joe Lewis kept his side in the game soon after Skuse's goal with a brave dive at the feet of City top scorer Nicky Maynard.
And Lewis was in spectacular action on 68 minutes when diving to his right to tip over Lee Johnson's 25-yard shot.
Substitute Danny Haynes fired just over for City in the closing stages before Boyd's' effort out of the blue deflated home supporters.