The club return to European competition for the first time since in a decade, when they reached the third round of the now-defunct UEFA Cup in the 2002/03 season. They will begin their first ever Europa League campaign in the second qualifying round.
Striker Wilfried Bony, who scored twice in the first leg at Waalwijk, netted his third of the play-off with just three minutes on the click at his home ground, the GelreDome.
Geoffrey Castillion gave Waalwijk, who defeated Steve McClaren's FC Twente in the play-off semi-final, a lifeline when he scored with 15 minutes remaining to make the aggregate score 4-2.
However, Waalwijk were not able to score even one of the two goals still needed for them to win, and Alex Ibarra's goal six minutes from time sealed victory both on the night and over the two legs for Vitesse.