Mislav Orsic scored a brilliant hat-trick as the Blues overturned a 2-0 first-leg deficit to script a memorable comeback victory.
Tottenham, coming off the back of a 2-1 loss to Arsenal in the North London Derby, were second best for most of the game.
Yet, this was unexpected. Jose Mourinho's Tottenham side had a healthy advantage and dominated possession too.
However, a troika of top-notch strikes from Orsic in the second-half, including a third in extra-time, wiped out Tottenham's lead and sent the Lilywhites packing.
It is Dinamo Zagreb who now go into the hat for tomorrow's quarter-final draw while leaving Mourinho on the brink of a sack and Tottenham in a mini crisis.
Here are the player ratings for Tottenham Hotspur:
Hugo Lloris - 6/10
Poor Lloris. He was beaten by three amazing goals on the night. The World Cup winner made one excellent block in the dying moments of the second extra-time but it was too little too late.
Serge Aurier - 5/10
He made five successful tackles - but that was about it for Aurier, who was otherwise miserable on the night while Orsic coolly stepped inside him for his first strike too.
Davinson Sanchez - 6/10
While his stats make for good reading - seven clearances (most by a Tottenham player) and six interceptions (most in the match) - the Colombian struggled with Orsic's pace from open play and was also beaten for his hat-trick goal.
Eric Dier - 5/10
He looked to be in no man's land in the defense as Dier made several poor passes in the match and offered no resistance either.
Ben Davies - 4/10
Limp in attack and awful in defense. That second Dinamo goal stemmed from his flank and the Welshman couldn't do anything.
Moussa Sissoko - 5/10
One reason why Tottenham were outclassed today was their inability to control the midfield and Sissoko takes the blame for that. He overhit his passes and gave away possession several times.
Harry Winks - 5/10
He didn't look too happy after getting subbed off but Winks cannot really complain given his struggles all night. There was no communication between him and Sissoko whatsoever.
Erik Lamela - 5/10
Much like his attacking counterparts, Lamela had a stinker, too. After his disastrous red card in the derby loss on Saturday, he was supposed to bounce back with a good performance, but did anything but.
Dele Alli - 6/10
Alli was promising during the opening exchanges, trying to link up with Kane and Lamela, though he was let down by a poor end-product. He faded into the match as it wore on.
Lucas Moura - 5/10
Did anyone even notice him play? Moura was virtually non-existent in the match and offered little to nothing going forward.
Harry Kane - 5/10
Another poor game from the Tottenham targetman who couldn't influence the game much and was unlucky to have seen two of his efforts saved on the line.
Gareth Bale - 6/10
He replaced the ineffective Lamela and brought some spark into the Spurs attack. One of his crosses also set Kane up but his effort was cleared off the line.
Giovani Lo Celso - 6/10
The Argentine returned from injury and made a promising cameo, adding some much-needed bite to Tottenham's attack.
Tanguy Ndombele - 6/10
He seemed eager to get involved in the mix but went ahead of his own skies at times.
Carlos Vinicius - 6/10
Vinicius had a few decent chances in the game but squandered all of them.
Sergio Reguilon - 6/10
The former Real Madrid man added some fresh legs and made a few good runs. But nothing substantial came of it.
Steven Bergwijn - 6/10
He fluffed a chance from a good position in extra-time.