On the exterior of the redecorated Emirates Stadium, Arsenal’s quadruple-winning women’s team of 2006-07 heave on red ropes, pulling up the former UWCL trophy. A trophy no other English team has won. That achievement is given equal billing opposite the men’s “Invincibles” team who are similarly raising high a gold Premier League trophy.

Related: ‘We lost by the tiniest of margins’: Jonas Eidevall hails his Arsenal side

Inside the stadium, the depleted Gunners battled valiantly but could not pull themselves into their second Champions League final, losing 3-2 against the two-time European champions Wolfsburg, with the winner coming deep into extra time.

There was no Beth Mead, no Vivianne Miedema, no Kim Little, no Caitlin Foord and no Leah Williamson and, ultimately, there wasn’t enough in the absolutely outstanding legs that remained, legs that gave everything for a record crowd of 60,063.

There were no changes to the starting XI that came from two goals down to secure a 2-2 draw in Germany, in part because the coach Jonas Eidevall’s options are extremely limited. Only Lina Hurtig was deemed ready to return to the bench, with Foord still “a little bit away from playing” according to Eidevall.

Wolfsburg welcomed back the captain, Alex Popp, who was kept out of the first leg with a calf injury, in place of Jule Brand but were also otherwise unchanged. The player of the match in the first leg, Jen Beattie, and Popp both started in the first meeting between Arsenal and Wolfsburg in 2013, a 2-0 defeat for the Gunners in front of 1,397 fans at Borehamwood.

It was almost the worst possible start for the hosts in a heaving stadium. Just three minutes in, the game was paused while VAR looked at a possible handball by Lotte Wubben-Moy. Fortunately for the England centre-back the player she was grappling with, Sveindís Jonsdottir, was offside in the build-up.

In his programme notes Eidevall had said that “when you’re successful with a comeback it gives the team belief that it can be done and that you can do it again”. The second-half comeback in the industrial city had done just that, and if there were any fears that Arsenal would replicate the limp first half there they were put to rest early on. The home team took a lead in the tie, for the first time, in style. Lia Walti’s incisive pass found Stina Blackstenius and the Swedish forward wrestled free of Kathrin Hendrich, rounded Merle Frohms and rolled the ball into an empty net. The celebrations had started before the ball had crossed the line.

Much like the visiting team in the reverse fixture, Arsenal failed to capitalise on their dominance of the first half. A ball over the top from Beattie allowed Victoria Pelova to race goalwards but her first touch was heavy, allowing a defender to clear as far as Noelle Maritz, who fired over.

The Gunners paid for their profligacy minutes before the break. A Svenja Huth free-kick, after Maritz was shown a yellow for dragging back Popp, was headed on by Popp to the former Gunner Jill Roord, who rattled her low shot through a maze of bodies and beyond the goalkeeper Manuela Zinsberger.

The goal flattened the sell-out crowd, but the fans roared back to life shortly after the restart when Blackstenius had the ball in the back of the net again only for it to be called back as Maritz was offside in the build-up.

Instead, Wolfsburg took the lead again just before the hour, a Felicitas Rauch corner headed powerfully in by Popp. It was a crushing blow to the Gunners who, in taking an early lead, had kick-started a narrative the crowd craved.

Blackstenius has shrugged off the noise of her doubters after the injuries to Mead and Miedema had heaped pressure on the Swedish forward. Since February she has scored the winner in the Continental Cup semi-final against Manchester City, the equaliser against Chelsea in the Continental Cup final, the winner against Bayern Munich in the quarter‑final of the Champions League and now in both legs of this semi-final. At the Emirates Stadium, though, her time was up, with her compatriot Hurtig replacing her.

In the 75th minute Arsenal once again levelled the tie, Wubben-Moy sweeping a partially cleared free‑kick back for Beattie to nod in. It was the goal that forced extra time, but only after Arsenal had another player fall, this time the substitute Laura Weinroither being taken off on a stretcher.

In extra-time Hurtig went close, with Frohms pulling of a wonderfully instinctive stop with her outstretched leg after the Swede had latched on to Maanum’s cross. The substitute Pauline Bremer flashed past the upright for Wolfsburg and Katie McCabe sent a strike glancing off the crossbar.

In the context of their battling performance, the way Arsenal conceded the decisive goal was crushing. Wubben-Moy was dispossessed by the substitute Brand who squared it for Bremer to slot in.

A crestfallen Wubben-Moy was comforted by her teammates and the crowd pushed them forwards in search of an injury-time leveller but it was one move too far. Arsenal are out, but they should not be down.