The scoreline flattered the Dons, who for long periods struggled to find any fluency to their play.
Despite their well-documented off-field problems, Gretna put up a spirited performance and frustrated the Dons right up until the last two goals midway through the second period.
With the game in doubt early in the week, Gretna came north and fielded a side which contained seven under 21s and four teenagers.
Aberdeen got off to a lively start and on two minutes Jeffrey de Visscher played a neat one-two with Lee Mller and his shot from 25 yards failed to trouble Artur Krysiak in the visitors goals.
The following 20 minutes the match mirrored Gretna's dire financial predicament with lots of effort but too many aimless passes.
Twenty minutes in de Visscher and Miller again linked up well, but the big striker's flick and shot on the turn was comfortably held by Krysiak.
The best chance of the match thus far fell to the visitors on 30 minutes. Ryan Baldacchino swept past Alan Maybury before playing the ball in to the near post where Ben Wilkinson's first-time effort was brilliantly beaten away by Derek Soutar.
Aberdeen finally made the breakthrough after 40 minutes, Gretna failed to clear a Ricky Foster cross into the area, de Visscher fed the ball into Barry Nicholson who played it into the path of Chris Maguire.
He showed good composure to plant the ball into the corner of the net for his first goal since Boxing Day 2006.
On 47 minutes Miller set up Scott Severin, whose crisp effort from 22 yards flew narrowly wide of the upright.
Minutes later a long-range effort from Maybury was spilled by Krysiak in the Gretna goal, but the home strikers failed to react allowing the keeper to smother the loose ball.
Aberdeen extended their led on 71 minutes when Miller beat the offisde trap to race on to a Foster through ball, as he rounded the keeper he was bundled to the floor to give Dougie McDonald an easy decision to award a penalty.
The Dons striker dusted himself down before firing home the resultant kick past the despairing dive of the Gretna goalie.
Aberdeen scored again in their next attack, Sone Aluko played a great ball up to Steve Lovell, who held the ball up long enough for Nicholson to slam his lay-off into the corner of the net from the edge of the area.
The Dons visibly relaxed and started to play some attractive football, but despite creating a number of good chances the scoreline remained 3-0 at the final whistle.