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Scotland's livewire fullback Stuart Hogg and Ireland's flyhalf and world player of the year Jonathan Sexton limped off in a close first half, during which the visitors outscored Scotland with two tries to one through Conor Murray and Jacob Stockdale.
Ireland, beaten by England in the opening game last weekend, added a third try after the break at Murrayfield as replacement flyhalf Joey Carbery sliced through a gap before flinging a wide pass for winger Keith Earls to score.
While Scotland hammered away at the Irish defence on a cool, clear afternoon that defied pre-game expectations of high winds from storm Erik, the home side could not add to a single try from centre Sam Johnson.
Ireland's captain Rory Best hailed a strong performance from Sexton's replacement Carbery, who recovered from throwing an intercepted pass for the only Scottish try to enjoy an influential second half.
"Joey is a quality player, you don’t want to see anyone go off injured, but it’s great to see everyone coming off the bench and stepping up,” he said.
The hosts will be disappointed not to have capitalised on a promising first half, with only a Greig Laidlaw penalty to show for their efforts after the break as handling errors constantly undermined some typically exuberant attacking play.
Scotland's captain Laidlaw expressed frustration with referee Romain Poite in a pitchside interview after the final whistle.
“We're disappointed. Handling errors cost us, but the referee doesn't seem to like us. We're not going to blame him, though. Ireland took their opportunities,” he said.
Scotland will have the opportunity for revenge on Sept. 22 when the two sides meet again in the opening round of the World Cup in Japan. The Celtic rivals will be desperate to top their pool and avoid a likely quarter-final against the mighty New Zealand.