Thomas Ince, with his second goal of the game, and Kevin Phillips struck in the 84th and 87th minutes to lift the Seasiders from seventh up to fourth in the table.
Jon Stead gave Bristol City a 29th-minute lead but Ince levelled things up 10 minutes into the second half.
The result extended the Robins' winless run to six league matches and saw them fall a place to 21st in the table, just three points above the relegation zone.
Injuries forced both managers to make wholesale changes.
City boss Derek McInnes swapped five players. With Kalifa Cisse, Cole Skuse and Marvin Elliott ruled out, on-loan Bolton midfielder Sean Davis made his debut.
Lewin Nyatanga's absence saw Jordan Spence and Louis Carey return in defence, while Chris Wood and Stead led the attack as Brett Pitman dropped down to the bench.
Chris Basham, Matt Phillips, Roman Bednar, Craig Cathcart and Gary Taylor-Fletcher all failed fitness tests for Blackpool.
Veteran striker Phillips, midfielders Ince and Angel Martinez and defender Neil Eardley all came into Ian Holloway's team.
A well-worked move resulted in Richard Foster firing wide after three minutes.
Stead chased down a ball over the top before warming the hands of Blackpool goalkeeper Matt Gilks.
Stead worked Gilks again in the ninth minute after Davis pounced on a mistake Angel Martinez.
It was third time lucky for Stead just before the half-hour mark. The striker turned his man inside the area and placed a left-foot shot into the bottom corner for his first goal since the final day of last season.
Wood went close to extended City's lead three minutes before half-time but Gilks got down well to smother his 18-yarder.
Blackpool were a little livelier when the game restarted.
Phillips won a free-kick, took it himself but hit it just wide. Most of the 815 Tangerines that made the journey thought their team had equalised.
Back at the other end, Gilks spread himself well enough to put off Albert Adomah and the forward dragged his shot wide.
The visitors were level after 55 minutes.
Phillips won another free-kick in a dangerous position. This time Ince took it and beat David James with the aid of a deflection.
The game had suddenly become stretched, with chances coming thick and fast at both ends.
James gathered an effort from Phillips on the hour before Adomah attempted a overhead kick.
Gilks reacted brilliantly to beat away a six-yard header from Wood, while James produced a superb finger-tip save to deny Ince after 70 minutes.
However, Ince did get the better of the former England goalkeeper again with six minutes remaining.
Substitute Brett Ormerod turned his man down the left and crossed the ball to the back post for Ince to tap home.
Phillips sealed the win soon afterwards. Ormerod was involved once more, playing the ball out to Stephen Crainey before Phillips knocked home from six yards out.
Alex Baptiste cleared one off the line in injury time to thwart City.