Some neat build-up play from Tyrone Mings and Paul Anderson led to the first chance of the game on nine minutes, with the latter crossing the ball into the box only for Jay Tabb's effort to be blocked, while Daryl Murphy's follow-up was well saved.
Novak and Clayton Donaldson both came close to getting Birmingham off the mark, but after a couple of narrow misses, David Edgar eventually turned home David Cotterill's corner at the back post to make it 1-0.
Connor Sammon came close to finding an equaliser with two chances in quick succession, only for his attempts to be thwarted by Edgar seven minutes before the interval.
The Tractor Boys levelled the contest up five minutes into the second half when Berra turned home Paul Anderson's free kick into the corner of the net.
Anderson almost added his name to the scoresheet shortly after with Darren Randolph being forced into a strong save to deny him.
The missed chance proved costly on 63 minutes, as Wes Thomas picked out Donaldson who subsequently placed the ball beyond Gerken to regain Birmingham's lead.
Lee Clark's side had a big shout for a penalty turned down late in the game when Paul Caddis went down inside the area, but the referee waved play on. It was to prove a huge decision, as with just seconds remaining Berra headed home his second goal to dramatically rescue a point for Ipswich.