After James Morrison saw his close-range shot pushed onto the post by home goalkeeper and captain Samir Handanovic at the Bonifika Stadium, midfielder Andraz Kirm gave Slovenia the lead in the 33rd minute with a header from Miso Brecko's cross.
However, six minutes later the Scots were back on level terms with a similar goal when Berra buried the ball past Handanovic from Charlie Adam's corner from the left.
The second half produced little goalmouth action at either end and that will be a worry to Craig Levein, from a Scotland perspective.
Morrison and Celtic winger James Forrest impressed but the lack of a goal threat will need to be addressed before the World Cup qualifying campaign begins in September.
Scotland will play Serbia at Hampden Park on September 8 and Macedonia three days later in Glasgow as they begin their bid to reach the 2014 World Cup finals in Brazil and the Scots boss will need goals by then.
There was an element of experimentation about Levein's selection.
Celtic defender Charlie Mulgrew was handed his debut, starting as left-back with stand-in captain Gary Caldwell partnering Berra in central defence.
Norwich's Russell Martin made his first start at right-back, with Allan McGregor in goal.
A midfield five of Adam, James Morrison, James McArthur, Forrest and Jamie Mackie backed up Craig Mackail-Smith, who was playing the lone-striker's role with Kenny Miller named on the bench.
The Scots went into the game hoping to build on their 2-1 friendly win over Cyprus in November but McGregor had to come to the rescue in the third minute when his defence went to sleep.
Slovenia midfielder Josip Ilicic split the Scotland rearguard with a clever pass to release Valter Birsa but the Rangers keeper raced from his goal to make the saving block at the edge of his box.
Moments later, at the other end, Mackie fired wide of the target from 25 yards and Levein's side were up and running with Forrest, in particular, looking in the mood on the left wing.
The guile the visitors needed came from Adam in the 26th minute when his superbly-weighted pass found Morrison racing into the Slovenia box but his close-range shot was touched onto the post by Handanovic, who gathered at the second attempt.
McGregor tipped a Birsa free-kick over the bar for a corner a minute later, which the Scots survived, before Morrison tested Handanovic again with an angled drive.
However, the ease in which the home side took the lead will have infuriated Levein.
Right-back Brecko easily managed to get his cross in past Mulgrew and Kirm rose high above Martin, who failed to react, to bullet his header past McGregor.
But six minutes from the break Adam's corner from the left -
the visitors' first of the game - found Berra at the back post and the Wolves defender sent his header from eight yards past Handanovic for his second international goal.
Barry Bannan replaced Adam for the start of the second half before the tireless Morrison had another attempt on goal in the 51st minute - his right-footed drive from distance clearing the bar.
Bannan, quick to emerge himself into the action, forced a decent save from Handanovic with a 25-yard drive three minutes later.
The game was swinging from end to end and the Tartan Army inside the tiny 4,200-capacity stadium held its breath every time the home side neared McGregor's penalty area.
Robert Snodgrass replaced Mackail-Smith just after the hour mark.
The early energy had gone, the tempo dropped and the substitutions began to disrupt the flow of the game.
In the 80th minute, though, Mackie came close when he headed a Snodgrass cross just past the post, before he was replaced by Miller.
Moments later, as the visitors' defending grew more desperate, McGregor was happy to see a drive from Zlatko Dedic take a deflection past his post for yet another Slovenia corner which came to nothing - and there was no further excitement in the closing stages.