The Serbian striker converted Shane Ferguson's cross from close range to clinch Blues' first-ever points at the Riverside and their first victory on Boro soil in 14 attempts stretching back to a 1980 success at Ayresome Park.
More importantly the victory moves Lee Clark's side on to 49 points and into the top half of the table.
Either side could have claimed three points from a finely-poised encounter which lacked clear-cut chances, although Blues goalkeeper Jack Butland twice made impressive saves to deny Scott McDonald and Adam Reach.
Boro - playing in front of their lowest league attendance since October, just 14,348 - are now five points off the play-off places while they have lost four of their last five and won just one of their last seven.
Having started the year in third place they have now dropped down to ninth and had the season started on January 1 then they would be propping up the table.
Both bosses rang the changes for this one, Tony Mowbray bringing in as many as seven new faces while opposite number Clark also rotated three of his XI from last time out.
Blues had a start to forget after making a hash of the kick-off before losing Jonathan Spector to injury after just four minutes, Keith Fahey stepping in for his first appearance since October having been on lengthy compassionate leave.
But the visitors soon settled into what was a low-key start to proceedings and began to look the more threatening against a Boro side obviously lacking confidence, Ravel Morrison and Wes Thomas shooting narrowly wide.
Thomas then latched on to Andre Bikey's short header but saw his shot saved by Jason Steele.
Boro grew in stature and enjoyed a solid period of pressure in which McDonald fired wide from 12 yards but, all in all, the game still lacked spark.
Fahey drilled just wide from distance before McDonald tapped the ball home at the other end only to be denied by an offside flag.
Both sides were looking increasingly dangerous as the first half wore on - Sammy Ameobi firing straight at Butland before McDonald blazed over, while Steele saved from Morrison - but it remained goalless at the break.
Middlesbrough failed to really test Butland during a string of corners at the start of the second half.
But the England goalkeeper had to be alert in the 57th minute to deny McDonald, who had been sent clear by a routine long ball.
The encounter took on an increased tempo after the break, largely due to greater urgency from the hosts, with substitute Ishmael Miller heading just wide before Nathan Redmond went just as close for Birmingham with a long-range effort.
Butland was again on call to palm away an effort from Reach before Morrison saw his shot parried away.
But the game's winning goal finally arrived nine minutes from time, Wade Elliott finding Ferguson who sent in a low cross which was converted by Zigic, who just got ahead of George Friend, to clinch City's first league double over Boro in 32 years.
- Sports & Recreation
- Jack Butland
- Scott McDonald