The Eagles had a host of opportunities to find the net throughout the evening but their inability to convert cost them a potential spot in the next round
The Portuguese paid the price for wasting an abundance of chances that could have seen them take a memorable three points against a largely second-string Blaugrana team, as a win for Celtic in Group G's other fixture meant they would have to settle for a spot in the Europa League.
Tito Vilanova sprung a number of surprises with his Barcelona line-up, but the biggest came as Messi, one strike away from equalling Gerd Muller's record of 85 goals in a calendar year, began the game from the bench.
After a brief attempt from Adriano to fill the Argentine's shoes with a scything run through the visitors' back line, a defensive lapse enabled Rodrigo to race through on goal at the other end.
The former Real Madrid youngster had Nolito in support but went alone and failed to bend his shot into the corner, instead watching it skip wide after 12 minutes.
It proved not to be a momentary slip as the Blaugrana defense looked extremely disorganized. In the 21st minute they did not pick up Nolito on the left and his cross found an unmarked Lima in the box. The Brazilian, however, was unable to direct his diving header on target and Pinto was untroubled.
Benfica continued to look more threatening but its profligacy in front of goal did not appear to be ending. Lima's shot came back off the post after the slightest of touches from Pinto, and John shot into the side netting after cutting inside Carles Planas with ease in the 35th minute.
The second half looked to be heading the same way as the first when, within the first minute of the restart, Nolito saw his curling effort from Lima's cross sail narrowly wide of the target.
The Catalan giants finally began to create some chances through David Villa but when those were not taken, Tito Vilanova introduced Messi in the 58th minute.
Yet the Argentine did not quite have the desired game-altering impact. After a rather tame 79th-minute free kick he was denied the fabled 85th goal following a great recovery save from Artur at the death, though he seemed to do himself some damage in attempting to find the net and he was subsequently taken off on a stretcher.
For Benfica the point was not enough to book a spot in the next round as it finished third, two points adrift of Celtic, while Barcelona finished on top of the pile.