Joe Ansbro's first international try four minutes from time and Ruaridh Jackson's subsequent conversion settled the contest in which neither side really impressed.
Jonathan Sexton kicked two penalties for Ireland while Scotland's Chris Paterson, winning his 105th cap, managed one for the hosts.
In a match that began 15 minutes later than scheduled as a result of crowd congestion, Ross Rennie made his first Scotland start while Graeme Morrison returned in a team showing five changes for the clash.
Flanker Rennie was joined in the back row by Alasdair Strokosch and Johnnie Beattie, with Jim Hamilton at second row in place of Alastair Kellock, who was named on the bench, while scrum-half Rory Lawson began the EMC Test at Murrayfield as captain.
Ireland started their first of four World Cup warm-up fixtures with flanker Mike McCarthy making his debut as part of a largely second-choice scrum and full-back Rob Kearney and scrum-half Tomas O'Leary making their comebacks from injury.
Ireland held a slender 3-0 half-time lead as both sides looked rather disjointed during the first match of the season.
Scotland suffered an early blow after just 21 minutes when Nikki Walker went off with a head knock, with Jack Cuthbert coming on for his debut after 21 minutes.
Sexton's penalty from in front of the posts in the 33rd-minute was all that separated the sides at the break after Jim Hamilton was penalised for killing the ball.
Little improved in the second period although Scotland managed to level the scores in the 49th-minute after Denis Leamy was caught offside, allowing Paterson to kick the subsequent penalty.
Ireland went back in front with 15 minutes remaining as Sexton kicked for goal from 45 metres following an offside.
Paterson, usually unerringly accurate with the boot, sliced a straightforward penalty attempt wide before going off as Nick De Luca came on as one of three substitutes.
An indiscretion from prop Al Dickinson, who earlier came on for Allan Jacobsen, at the scrum granted Sexton another shot at goal, but the Ireland fly-half's effort fell short.
Scotland then burst into life four minutes from the end when De Luca rushed through before a long pass to Ansbro, who cut in off the wing for his first Test try.
Jackson converted successfully to seal victory.
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