Andy Keogh had put Blackpool deservedly in front at the interval, but a superb strike from Novak levelled the teams up in the 63rd minute.
And after Blackpool defender Jack Robinson was sent off late on, the Birmingham pressure eventually told and Novak headed in to secure a second league win of 2014 for Lee Clark's side.
It was another blow to the slumping home side, who remain under the caretaker management of former Birmingham midfielder Barry Ferguson.
The visitors spurned a great chance to take the lead after only two minutes as Novak found Federico Macheda who missed his kick with the goal gaping.
The Manchester United loanee had another chance two minutes later but headed over when left unmarked and just eight yards out.
Faris Haroun then had a golden opportunity to put Blackpool in front at the other end but the Belgian fired over.
The home side went close again in the 12th minute as they sliced Birmingham open through Haroun, who found Keogh but the Irish striker poked wide.
Birmingham goalkeeper Darren Randolph was then forced into action for the first time to push Kirk Broadfoot's header over the bar.
Keogh put the home side in front when the ball broke to him after a corner and the on-loan Millwall striker put the ball beyond Randolph with a volley into the far corner.
That was how it stayed until the interval but Birmingham had a golden chance to draw level in the second minute after the break. Chris Burke was put clean through by substitute Nikola Zigic, but goalkeeper Matt Gilks denied the winger.
Zigic then had a great chance himself to pull Birmingham level after 55 minutes, but when confronted with Gilks he tried to chip the Blackpool goalkeeper and only managed to dink the ball meekly into his arms.
Birmingham drew level when top scorer Novak fired left-footed and high to the left of Gilks from the edge of the area after a knock-down from the influential Zigic.
Blackpool were then reduced to 10 men in the 75th minute as Robinson was shown a straight red for bringing down substitute Jordon Ibe as he was clear through on goal.
Ibe, who joined on loan from Liverpool on Friday, continued to threaten as he cut in from the left and forced Gilks to save his low shot.
Blackpool were clinging on but eventually Clark's troops had their winner as Novak netted his second of the game in the 82nd minute, heading low beyond Gilks from an Emyr Huws cross.
Late on Blackpool pushed hard and Haroun went close to an equaliser but it was not enough as Birmingham earned another impressive away result.