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After 133 seconds, Darwin Nunez opened scoring for Benfica
Ronald Koeman stated that it was not a good idea to compare his Barcelona team with those of the past, after Benfica's defeat made this the worst Champions League start for the club.
Barca, which was also beaten by Bayern Munich 3-0 earlier this month, has lost its opening two matches of the competition for the first-time and is currently at the bottom of Group E.
Benfica started energetically and scored within three minutes. Darwin Nunez then cut in and finished low in the corner.
Rafa Silva scored a second goal after the break, and Nunez won a penalty to secure a comfortable win for the home team.
Koeman, a member of the Barca team that won the European Cup 1992, said: "I'm going to not argue about the level my team."
"It's futile to compare this with the Barcelona teams of years past. It's as simple as water. My opinion about my work at the club is limited. I feel supported by my teammates and their attitude.
Nunez scored two goals and also hit the post wide after rounding Marc-Andre ter Stegen (Barcelona goalkeeper) who had made a rash move to charge out of his zone.
Luuk de Jong missed an excellent chance to equalize for the visitors in the first period when he was presented with an open goal.
Barca failed to score a single goal and Eric Garcia was sent off with three minutes left.
"Benfica are strong and quick. Koeman said that Koeman felt the team had to do a better job of defending for the first and second goals.
"We had some really good scoring opportunities and that's what can change the match's direction." It was the fact that Benfica lost the majority of the chances that they created that made the difference.
Koeman's Barca: Unwanted History
Koeman is now in charge of one the most successful clubs in Europe during one of the toughest periods in their recent history.
This side is far from the club that won Europe's most-sought-after club prize in 2015, due to its financial difficulties, which were highlighted by Lionel Messi's departure to Paris St-Germain.
Five-time Champions League winners will be unable to participate in the Champions League knockout stage. This is the first time they have not been included since 2003-04, when they were not eligible for competition.
They failed to advance from the first stage of the competition's group stage in 2000-01. This is also when they suffered consecutive group defeats to AC Milan and Besiktas.
Barca has lost its opening two European matches this year to Benfica and Bayern in Group E. This is the first defeat since the 1972-73 Uefa Cup when they were defeated in both legs in Porto.
They also conceded six goals in the process. Only one team has ever advanced with such a bad record - Lyon, who reached 16 in 2007-08.
Koeman managed eight games in the Barcelona group as Barcelona boss, but Louis van Gaal has suffered more losses with five defeats in 32 matches than Louis van Gaal's three group-stage fixtures.
Barcelona has lost four of their five Champions League matches and drawn the other. This is more than they have lost in any of their 39 previous matches.
They will next be hosting Dynamo Kyiv who are currently one point ahead of them after an opening draw against Benfica. Koeman knows that a win would likely spell the end for his European hopes and possibly his tenure as manager.