The Spanish club won 80-67 to finish the Euroleague's group stage with an 9-1 win-loss record, one game clear of second-placed Fenerbahce, while Panathinakos (5-5) finished third in Group C.
The Olympic Sports Centre in Athens was evacuated at half-time due to an alleged bomb threat, resulting in a one-hour delay.
Barcelona led 40-23 when the game eventually resumed but that lead was quickly reduced as Vlantimir Giankovits and James Gist inspired Panathinaikos to drag the hosts as close as 53-47 during the third quarter.
The visitors rallied, however, and broke even in the final term to claim a 13-point victory.
With second-placed Fenerbahce having overcome Bayern Munich 87-81 earlier in the day, a loss for Barcelona could have seen them drop to second, although their healthy points difference saw them likely to stay top.
But with Marcelinho Huertas (17 points, nine assists) and Maciej Lampe (10 points, 10 rebounds) impressing for the visitors, they advanced to the Top 16 with some momentum.
Antonis Fotsis (14 points) top-scored for Panathinaikos.
In Turkey, Fenerbahce kept Bayern to less than 20 points in the opening two quarters to set up their victory.
The home side led 42-33 at half-time and then matched Bayern blow for blow in the second half to win by six points, with Bogdan Bogdanovic top-scoring for Fenerbahce with 16 points.
In Group A, James Anderson notched a three-point play with 2.5 seconds remaining as Zalgiris defeated Dinamo Banco di Sardegna Sassari 80-79 to secure their spot in the next round.
Zalgiris led 29-18 after the first quarter but had their lead reduced to just two points with a period to play as Dinamo Sassari fought back.
In a dramatic final quarter, Dinamo Sassari claimed a late two-point lead when Cheikh Mbodj sank just one of two free-throws but Anderson's late heroics saw Zalgiris (5-5) claim third in Group A, pushing UNICS out of the Top 16.
Earlier, Nizhny Novgorod had defeated UNICS 78-74 to book a spot in the next phase, while in Group B, Cedevita defeated Alba Berlin 70-67 and in Group D, Crvena Zvedza trumped Laboral Kutxa 90-82.