Benfica thrashed Maccabi Haifa 6-1 on Wednesday night to wrest top spot in Champions League Group H from Paris Saint-Germain.
PSG and Benfica were both through to the last-16 before their final group games and were level on 11 points having drawn both of their meetings 1-1.
However, PSG led the pool boasting a better goal difference of four.
Kylian Mbappé and Nuno Mendes were both on the scoresheet in PSG's 2-1 victory over Juventus in Turin.
But Benfica's mauling of Maccabi in Israel left the sides deadlocked on 14 points with 16 goals scored and seven conceded.
It was the first time in the 30-year history of the European football's most prestigious club competition that two teams had finished with an identical record.
Record
Benfica took the honours because they had scored more goals in away ties than PSG.
It means that on Monday's draw for the knockout stages, PSG could be paired against the likes of holders Real Madrid, Manchester City and Bayern Munich - teams that have thwarted their Champions League ambitions over the last three years.
"We've got through but we would have liked to be first," Mbappé told French broadcaster Canal +.
"We did all the work for that but finishing second and the way it happened is just part of football.
"We're going to look forward to the last-16 when it happens next year."
Madrid eliminated PSG in the last-16 on their way to a record-extending 14th triumph in the European Cup/Champions League.
Elsewhere in the competition, France international Olivier Giroud bagged a brace as AC Milan beat FC Salzburg 4-0 to secure second spot in Group E behind Chelsea.
RB Leipzig claimed the runners-up spot in Group F with the same scoreline against Shakhtar Donetsk.
