Both teams have performed well in qualification so far. Scotland sit third in Group D with seven points going into Sunday's clash with Gibraltar while Northern Ireland are second in Group F with three wins from four ahead of a home game against Finland.
It was the hosts who eventually claimed a deserved triumph in Glasgow, edging a contest that provided little in terms of entertainment.
Manchester United's Jonny Evans captained Northern Ireland - in his first appearance since receiving a six-match ban for spitting at Newcastle United's Papiss Cisse - and it was his defence that received the sterner test as Scotland created the better opportunities during a dour affair.
Indeed, Scotland - who beat the Republic of Ireland in their last qualifier in November - perhaps would have claimed a more comfortable win had they not found Northern Ireland goalkeeper Michael McGovern in good form.
McGovern appeared equal to everything thrown at him by Gordon Strachan's side, but five minutes from time Berra settled things with a header into the bottom-right corner.
Scotland started brightly and would have taken the lead in the fourth minute if not for the reflexes of McGovern.
Hamilton Academical goalkeeper McGovern produced a low stop down to his right to deny Sunderland striker Steven Fletcher following good work from Ikechi Anya.
Anya was Scotland's most dangerous player in the first half and drew another save from McGovern before then firing wide following a quick counter-attack.
The hosts continued to dictate matters but found McGovern in good form, Fletcher again thwarted after a precise Shaun Maloney pass.
There was no let-up in the pressure from Scotland upon the restart but they also remained profligate, with substitute Steven Naismith heading over from Craig Forsyth's left-wing cross.
Jordan Rhodes was thrown on for Scotland in the 63rd minute for his first international appearance since 2013.
Forward Josh Magennis then flashed an effort wide in a rare chance for Northern Ireland, but they were on the back foot for the majority of the encounter and McGovern was forced into action again as Naismith headed straight at him from a corner.
Scotland's chance of victory appeared to have passed, yet Berra took advantage of some poor defending to grab a late winner.
The centre-back met a corner from Matt Ritchie - making his first visit to Scotland after receiving a maiden call-up from Strachan - with a precise header that defender Lee Hodson failed to clear off the line as the hosts' pressure finally told.
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