Making an astonishing 124th consecutive appearance for Posh, Boyd headed in from Danny Rose's cross in the final minute to send the visiting fans into raptures.
It was no more than Posh deserved after dominating for long spells against a Bristol City side who had gone ahead on the half-hour mark through Cole Skuse.
Bristol City goalkeeper Dean Gerken made good saves to deny Craig Mackail-Smith and Shaun Batt in the second half before Boyd earned Posh a share of the spoils.
The result continued Bristol City's unbeaten league record at Ashton Gate this season, while struggling Peterborough are still looking for their first away league win.
The home side made a good start and Nicky Maynard had an early sight of goal but fired over the bar.
However Peterborough should have opened the scoring minutes later when Boyd sent Mackail-Smith clean through but Gerken made a good stop.
Posh continued to play some attractive football and Rose dragged a shot wide from the edge of the area before squandering a second chance when he blazed over after Lewin Nyatanga failed to clear.
With half an hour gone Bristol City made Peterborough pay for their proligacy when Skuse was given time to run at the defence and he got past two challenges before firing beyond Joe Lewis.
It could have been 2-0 moments later but Lewis made an excellent save to deny Maynard from close range.
Peterborough continued to push for an equaliser and on the stroke of half-time the Bristol City defence failed to deal with Gabriel Zakuani's corner but Louis Carey made a superb goal-line block to deny Rose.
The visitors picked up where they left off in the second half and Chris Whelpdale fired over from 25 yards.
Just before the hour mark Boyd's excellent cross found Mackail-Smith six yards out but his shot was superbly kept out by Gerken.
Darren Ferguson's men were dominating proceedings and Batt let
fly from 20 yards but his shot was blocked by Jamie McAllister
However, the Robins gradually found their rhythm once again and Lee Johnson's shot from 25 yards looked to be heading in but Lewis got across his goal well to tip the ball around the post.
Jamie Day then fired over from 25 yards for Peterborough before flashing a cross-shot across goal but no-one was on hand to turn the ball in.
The game began to open up and Lewis had to be alert to keep out Evander Sno's 25-yard effort which skidding along the surface.
It looked as if Bristol City were heading for all three points but in the final minute of normal time Rose's cross found Boyd and he headed past Gerken.