The Dons were handsome 3-0 winners in Croatia last week and looked to be cruising to the next phase after controlling much of the first half.
Yet they suddenly found themselves on the back foot as they conceded two goals in five minutes and only settled again when Niall McGinn pulled one back almost immediately.
Jonny Hayes later levelled to ensure a 5-2 aggregate victory which means Derek McInnes’ team now travel to FC Kairat in Kazakhstan for their first game at the next stage on July 30.
Aberdeen’s success on the Adriatic coast seven days ago was the result of a mature, disciplined performance but McInnes was adamant before kick-off a job still had to be done.
His team selection reflected that, with any questions of complacency eradicated as he made only one change to the side which won so handsomely last time out.
With the Dons well ahead, they had no need to press in the early stages and that made for a low key start to the match.
In fact, all the drama came after the break but when Marin Tomasov broke the deadlock for the Croatian side from the right, it did little more than raise eyebrows.
There was more concern as a deathly silence enveloped the ground soon after when Zoran Kvrzic’s deflected shot went in just after Hayes had missed at the other end.
Aberdeen’s response was hugely creditable and Northern Ireland international McGinn’s fine finish off the post from a low David Goodwillie cross was a relief for the home side as much as anything.
The majority of the 15,803-strong crowd were able to relax much more when Hayes found the net too with 20 minutes left.
Goodwillie was once again the provider as he made great progress down the left then set up his team-mate, who slotted well past goalkeeper Simon Sluga.
With that, a rash of substitutions from McInnes suggested he felt the tie was won and a tame finish to the game showed Rijeka knew their chance was gone too.