A penalty from Adam Rooney and another strike from Niall McGinn in a seven-minute spell put the Dons 2-0 ahead on aggregate in the second qualifying round tie before Maikel Kieftenbeld pulled a goal back a minute before the break.
McInnes had been confident ahead of the trip to the Netherlands that his side would score, following last week’s goalless draw at Pittodrie.
And despite second-half pressure, Aberdeen held on to their lead to set up a tie with Spanish club Real Sociedad in the third qualifying round.
"It was a special night for the supporters to come and see their team win," McInnes told a Scottish radio station."I always feel, whether we are an underdog or the favourites, we always put in a shift. It is a big result but to be honest it's no more than I expected. I always felt we could win here."