Sunderland's Kevin Kyle put the Scots ahead early on and Steven Thompson added a second before the break. Christian Dailly and Scot Gemmill were on target in the second half.
Both Boro players had a chance to get on the score sheet, first Johnston was blocked by a late tackle after a good run, then Stockdale saw his powerful drive hit the side netting.
Meanwhile Boro target Benni McCarthy was the hero for South Africa as he netted two second half goals against Turkey. McCarthy scored with practically his first touch, after coming on as substitute with an hour gone, then wrapped the game up in injury time.
The victory was enough for South Africa to win the Reunification Cup.