The Rams got off to a dream start when Patrick Bamford scored with just 34 seconds on the clock.
But a spectacular strike from Crystal Palace loanee Jonny Williams drew Ipswich level before Berra's late goal made it 2-1 at Portman Road.
Derby had started the match just as they ended their last Championship encounter - a 5-0 hammering of local rivals Nottingham Forest.
Just 34 seconds had elapsed when Craig Forsyth found space down the left and his low cross was turned in by Bamford.
A hard-fought 20 minutes ensued with Derby's Chris Martin going toe-to-toe with Berra in an incident which saw the Town defender go to ground and the striker shown a yellow card.
Bamford was proving to be a real handful for the home side and his low shot after 27 minutes was well held by Dean Gerken at his near post.
But the first half was largely forgettable with the match littered with fouls and Ipswich playmaker Williams targeted by some rough defending from Derby - a fact not lost on Town boss Mick McCarthy who had words for referee Fred Graham as the players went off at the interval.
The visitors had a great chance to double their advantage in the 52nd minute when Bamford found himself through on goal but his attempted chip over Gerken was thwarted by the Town keeper.
Minutes later, Ipswich found a way through the Derby defence as Williams broke clear down the left but Luke Chambers just failed to make a clean contact to the playmaker's clever chip.
On the hour mark, Town finally carved out a shot at goal as Anthony Wordsworth and Paul Anderson combined to release Daryl Murphy and his deft right-footed shot was tipped round the post by Lee Grant.
McCarthy introduced attacking firepower in Sylvan Ebanks-Blake and Frank Nouble, but Derby hit back with half-chances through Jeff Hendrick and Forsyth before Ipswich grabbed an equalizer out of nothing in the 68th minute.
Aaron Cresswell laid a short free-kick off to Williams who found the corner of the net from almost 30 yards.
Derby almost restored their lead in the 73rd minute when Martin's low cross was turned goalwards by the dangerous Bamford but his shot went agonisingly wide.
They went even closer two minutes later after Nouble's poor pass led to Forsyth breaking clear but his fierce drive cannoned off the near post.
The post then came to Derby's rescue when Ipswich's two subs combined, Ebanks-Blake striking the woodwork with a header from Nouble's teasing cross.
But Ipswich claimed a winner in the first minute of stoppage time, Berra rising highest to meet Cresswell's corner to send the ball past the diving Grant.