Dimitrios Diamantidis won the game MVP as he missed just one shot all night, scoring 15 points while also controlling things from the point guard position.
Six Panathinaikos players scored in double figures with Ramunas Siskauskas top scoring with 20, while Euroleague MVP Theodoros Papaloukas scored 23 points in defeat against his countrymen.
The Greeks were in complete control with a minute and a half to go as they led by eight but then two massive three pointers from the previously out of sorts Trajan Langdon seemed to put the defending champions back into the match.
A big fade away jumper by Michael Batiste put the Greeks 89-85 in front with 35 seconds to go before Langdon missed another three and Matjaz Smodis could just make one at the line after being fouled going for the rebound.
Milos Vujanic then downed two at the line for Pana and at 91-86 Langdon missed another chance at a three, but Siskauskas couldn't ice the game with two missed free-throws and Papaloukas raced down for a quick two to make it 91-88 with six seconds to go.
However, the Russians were forced to foul Siskauskas again and this time the Lithuanian made both to clinch the match, with a buzzer beating three from JR Holden proving a mere consolation for CSKA.
With 18,000 screaming Greeks in attendance it was perhaps not surprising that the home side settled quicker although in truth, both sides looked nervy in an opening five minutes littered with turnovers.
Diamantidis then started working the point well for Panathinaikos and nearing the end of the first quarter they had built up a 16-8 advantage.
However, big Slovenian Smodis then started to show some soft hands inside for CSKA as they went on a little run of their own and by the end of the first quarter the gap was down to one, with the Greens leading 18-17.
In the second quarter the game completely opened up as the two defenses went missing.
It looked like it was going to be a shoot-out at one stage but while Panathinaikos' pick and roll continued to cause problems, CSKA's offense slowed down and the Greeks built up a nice 46-36 lead by half-time.
However, in the 3rd quarter they couldn't get anything going on offense and didn't make their first field goal until there was just 2.50 left in the quarter.
At the other end Papaloukas caught fire for CSKA with the Russians even going briefly into the lead at one stage.
However, Panathinaikos' defence really started to step up near the end of the quarter and the offense was making lots of shots at the line which got them back in front and they led 65-57 going into the final quarter.
Both benches then had to do some major shuffling as a number of players on both sides got into foul trouble, but solid shooting from the line was keeping the Greeks well in front as the clocked ticked on.
Then came Langdon's two three pointers and all the late drama, but Siskauskas' late free-throws put the home crowd into ecstasy.
Nobody looked happier at the finish than Panathinaikos' Serbian coach Zelimir Obradovic who has now won six European Cups in his illustrious career.