Aberdeen made one change from the team that drew 1-1 with Celtic in the Scottish Cup on Sunday, as Nicholson replaced the injured Jamie Smith.
Gretna, who entered administration this week, had an unfamiliar look after several first-team regulars refused to play in the absence of medical insurance.
The side showed six changes from the defeat by Dundee United as Krysiak, Rostyn Griffiths, Ben Wilkinson, Abdul Osman, Ryan Baldacchino and Henry Makinwa were all handed starts.
Gavin Skelton dropped to the bench, while Greg Fleming, Chris Innes, John Paul Kissock, Mickael Buscher and Craig Barr were not named in the squad.
Aberdeen started brightly and Jeffrey de Visscher had the first shot on goal in the second minute, an effort comfortably saved by Krysiak.
Gretna managed to field a side against Aberdeen
Gretna struggled to retain possession and failed to give lone striker Makinwa any decent service.
The visitors did give Aberdeen a scare in the 36th minute when Baldacchino's cross was flicked towards goal by Wilkinson, but Derek Soutar saved well.
Maguire fired the Dons in front with an impressive drive just as it seemed the first-half would finish goalless.
Gretna rallied after the break but found it difficult to breach the Aberdeen defence.
And the Dons extened their lead in the 67th minute when Miller was felled in the box by Krysiak and the striker took the spot kick to score.
Nicholson made it three moments later when he collected Steve Lovell's pass before arrowing a superb shot past Krysiak.
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