The Dons warmed up nicely with a victory before travelling to Macedonian capital Skopje to take on Shkendija in their first round first-leg qualifier in mid-week.
An Adam Rooney penalty 20 minutes from time was enough to separate the sides at Brechin City’s Glebe Park.
Despite a competitive first half, neither side managed to carve out many clear cut chances as the teams went into the half time break on level terms.
Aberdeen boss Derek McInnes used the friendly to give new loan signing from Liverpool Danny Ward some game time, with the goalkeeper coming on at half-time.
Again, there were few clear cut chances at either end after the break with the deadlock finally being broken just after 70 minutes when Niall McGinn was brought down in the area.
Rooney stepped up to take the resulting spot kick, sending Alan Mannus the wrong way.
St Johnstone begin their own Europa League campaign against Armenian side Alashkert FC a week after the Dons.