A third defeat of the campaign for Madrid, coupled with wins for Barcelona, Chelsea, Sporting Lisbon and Manchester City, meant Madrid missed out on the top eight and will have to play in the two-legged knockout play-off round.

"We knew where we were coming from, what we were coming into, how difficult it would be, and obviously it got the better of us," new Madrid coach Alvaro Arbeloa told Movistar.

"I think we were far from the level we need to show.

"I've said it these past few days: we've got a lot to improve."

Benfica, on the other hand, will not turn their noses up at the extra games after 'keeper Trubin sensationally nodded in a 98th-minute goal to snatch the last qualification spot on goal difference.

Earlier, Kylian Mbappe netted a brace as Andreas Schjelderup scored twice and Vangelis Pavlidis converted a penalty for the hosts.

For Mourinho, who coached Madrid between 2010 and 2013, it was a first victory at the second time of asking against his old club since departing them.

"I think it was deserved, really deserved... for Benfica it's an incredible prestige to beat Real Madrid," Mourinho said.

Friday's draw will reveal if Benfica face a rematch against Madrid or 10th-placed Inter Milan, with whom Mourinho won the competition in 2010.

"I can't say I prefer one or the other because going to Madrid I like a lot and I've not gone there, to go to Milan I like a lot and I don't go there either," he said.

"Madrid and Inter are teams who can win the Champions League, and we are a team who at most can do something incredible."

Much the livelier side in the opening period, Benfica thought they had a penalty on the quarter-hour when the referee pointed to the spot following a Jude Bellingham challenge from behind on Gianluca Prestianni but the decision was overturned on review.

Mourinho was left shaking his head again moments later as Prestianni popped up in space on the left of the Madrid box and shaped a fine curling effort for which Thibaut Courtois needed all of his two-metre frame to tip onto the crossbar.

Mourinho's side soon, however, paid for their profligacy as Mbappe brought his Champions League tally this term to 12 goals with a clinical back-post header on the half-hour.

But next it was Madrid who were made to pay for over-confidence as the Portuguese side caught them desperately short on the counter six minutes after their opener.

- 'Historic goal' -

Raul Asencio was the only navy-shirted player in the Madrid half as Benfica launched into a counter, but the Spaniard was left slipping and sliding on the turf as Pavlidis went past him and centred for Schjelderup to nod home.

The home side then got the lead their performance deserved after Aurelien Tchouameni was penalised for a shirt pull on Nicolas Otamendi from a corner and Pavlidis stroked the resulting spot-kick straight down the middle five minutes into stoppage time.

The hosts won the ball and sprang forward on 54 minutes, with Schjelderup supplying another clinical finish after cutting past Asencio on the edge of the box.

Rodrygo Goes replaced the ineffectual Franco Mastantuono in the immediate aftermath and the Brazilian combined out wide with Arda Guler to set up the unmarked Mbappe, who unerringly fired home from 15 yards in the 58th minute.

The clock ticked into the final 20 minutes with everything still in the balance and Benfica's presence in the knockout play-offs fluctuating with results elsewhere in Europe.

Aided by Madrid going down to nine as Asencio and Rodrygo received late dismissals, Benfica looked set for heartbreak as they were sitting in 25th place, level on nine points with Marseille but with fewer goals scored.

The Estadio da Luz then erupted deep in injury time as Trubin turned the unlikeliest of heroes as he nodded in from a free-kick to send Benfica through.

"We were lucky to get a set-piece where Trubin, at two metres tall, goes up there and scores a fantastic goal, a historic goal, a goal that nearly brought the whole stadium down -- and I think it was very deserved for us," Mourinho said.