The Bundesliga side would have won the group if it had picked up all three points.
Bayer Leverkusen missed out on top spot in UEFA Champions League Group C following a 0-0 draw at bottom club Benfica on Tuesday.
The German club's place in the last 16 had already been sealed by Zenit St Petersburg's 1-0 win over Benfica on matchday five, but first position, and an easier path to the quarterfinals, was still to play for.
In the end, though, it was frustrated by the Portuguese champions, who failed to move off the bottom of the pool despite the battling result. And with Monaco winning 2-0 against the Russians, it was the Ligue 1 outfit which climbed to the summit and surged into the knockout rounds.
Leverkusen triumphed 3-1 when these two sides met in Germany back in October, but it was Benfica which went closest to finding the breakthrough this time around - Lima rattling the crossbar in the first half of a game lacking in goalmouth action.
Both managers employed somewhat experimental lineups, with Leverkusen leaving out regulars Son Heung-min and Stefan Kiessling while Andre Almeida was Benfica's only player retained from the weekend win against Belenenses.
As might have been expected given the contrast in what the two sides had to play for, it was the visitors who dictated the early play - albeit without finding the final ball.
But Benfica carved out the first real opening on the counterattack after 11 minutes. Ola John led the breakaway down the left and his cut-back was parried by Bernd Leno into the path of Lima, who, with the goal gaping just seven yards away, somehow managed to hit the top of the crossbar.
2002 finalist Leverkusen appeared susceptible to such pace in the wide areas, while it continued to make poor decisions in attack. That was almost its undoing in the 41st minute.
Once again, the visitors were caught in possession and could not contain John, as the winger evaded several challenges before threading a ball through to Lima, only for the striker to drag his effort wide when one-on-one with Leno.
There was still time in the first half for Bebe to flash a powerful effort across the face of goal from 18 yards, with Leverkusen fortunate to go in at the break level.
Roger Schmidt's side emerged with improved intensity in the second half, which in turn brought it more possession.
But the Germans remained limited to shots from distance and the closest they went was a 62nd-minute fluke deflection as Cesar's attempted clearance rebounded back off Roberto Hilbert and bounced just past the post.
The game descended into a sequence of scrappy challenges from there, as Leverkusen's grip on top spot loosened.
Its frustration boiled over in the 90th minute when captain Omer Toprak was shown a second yellow card for a needless and lazy challenge on the halfway line, compounding the side's disappointment.