The TV ad, created by The Union, showed an image of a young girl's head set against a black background with a voiceover and on-screen text stating: "Would you allow your organs to save a life? You have 20 seconds to decide."
The girl's face then started to fade gradually and become distorted and the voiceover said "Kill Jill?", accompanied by an on-screen of choice "Yes" or "No". The voiceover then said: "No... register and you could save a life".
The Advertising Standards Authority received 10 complaints from viewers who objected that the ad was misleading, offensive and distressing because it implied that people who did not register as organ donors were killing someone.
One viewer, whose seven-year-old son had been upset by the ad, objected that it was likely to cause distress to children.
The Scottish Government said that its aim was to motivate individuals to sign up to the UK organ donor register, not to offend or court controversy with its advertising.
It said analysis of previous softer campaigns had shown that it was difficult to spur people into action and get them to sign up for something that involved an unpleasant subject matter.
The Scottish Government also said that the ad was not misleading because there was a direct correlation between the number of people on the register and the number of organs available for transplants.
The ASA did not uphold the complaints because it considered most viewers were unlikely to interpret the claim literally and would understand the ad was intended to highlight that by signing up to the register they could save someone's life, which was made clear in the statement "register and you could save a life".
It considered that in the context of the important message the ad was promoting, it was unlikely to mislead, cause serious or widespread offence or undue distress.
The advertising watchdog also rejected the complaint about it causing distress to children noting that it had been given an ex-kids restriction, which helped prevent it being seen by very young children.
It concluded that it was not necessary to impose a greater restriction to direct the ad away from all children and that it had been appropriately scheduled.