We took the lead through Jack Roles at the Ulrich Haberland Stadion - next door to the BayArena - but were ground down by the home side in the second half.
Jakub Bednarczyk levelled on 57 minutes and having seen Tashan Oakley-Boothe rattle the crossbar, Leverkusen forged ahead via Anton Walkes' own goal 10 minutes later.
It stayed that way until added time when Tim Handwerker was bundled over by left-back Jaden Brown and picked himself up to convert from the penalty spot.
The result means we're yet to put any points on the board after three games in Group E.
There were only a couple of efforts of note - Oakley-Boothe's shot deflected wide, Guven Yalcin's 20-yarder straight at Alfie Whiteman - before we took the lead with a well-crafted goal on 18 minutes. George Marsh picked out Brown with a crossfield pass right to left and the full-back delivered a cross that simply asked to be converted. Enter Roles, who showed the desire to get across goalkeeper Tomasz Kucz and divert home.
Leverkusen started to take control at the midway point of the half and created three chances - although we played a part in all of them. On 23 minutes, we lost possession in our half and one pass later, Atakan Akkaynak was through on goal. He prodded past the advancing Whiteman and just wide of the post. Brown then miscontrolled a punt forward, Bednarczyk found Guven Yalcin, only for the striker to fire wide. On 35 minutes, Kyle Walker-Peters' pass was picked off by Guven Yalcin, he stepped wide of Walkes and measured a low shot from 18 yards that Whiteman did well to turn aside.
Above: Our players celebrate after Jack Roles' opener.
There was one more chance each before the break. Whiteman stood firm again to block from Guven Yalcin before Shayon Harrison had Kucz at full stretch with a 25-yard piledriver after winning a 50-50 with Simon Rhein.
Leverkusen stepped up again at the start of the second half and after going close twice - Sam Schreck's curler just wide, Cedric Harenbrock's shot blocked by Japhet Tanganga - levelled on 57 minutes. Handwerker got onto a big switch from Rhein, Tracey looked to have held him up but he managed to cross and find Bednarczyk, who planted past Whiteman from 12 yards. We almost found an immediate response as Oakley-Boothe slid in to win possession. The ball was worked wide and then back to him by Tracey and Oakley-Boothe shaped a curler over Kucz that came back off the crossbar.
That was rare respite, however, and Leverkusen took the lead on 67 minutes. There was more than a touch of misfortune about it as Hajdar Shala crossed low from the right, Walkes slid in to intercept, only to divert the ball past Whiteman and into the far corner. Whiteman had to be on his toes again three minutes later to deny Schreck.
There was certainly no lack of spirit as we chased an equaliser and pushed Leverkusen back in the final 15 minutes. However, there was only one more serious effort when Brown's cross was deflected and looped high towards the far corner, Kucz at full stretch to claw it to safety.
To rub salt into the wounds, Brown clattered Handwerker in the first minute of added time and Handwerker made no mistake from the penalty spot for 3-1.
JOHN MCDERMOTT, HEAD OF PLAYER DEVELOPMENT, SAID
“I think you have to give credit to Bayer Leverkusen – they were excellent, without doubt the best team and group of players we’ve played in the last six to 12 months. The disappointment is when you come away, you want to stay in the game and just tough it out. We didn’t control the ball as well as we could have done. We showed good bits of play at the end but by then we were chasing the game. We’ve got to have that grit and resilience to stay in it. We went 1-0 up, hit the crossbar and we can talk about ‘what ifs’ but today they were better man for man and we have to give them credit, as difficult as it is to say that.”
Bayer Leverkusen: Kucz, Shala, Handwerker, Rhein, Boeder, Nesseler (c), Bednarczyk, Akkaynak (Grym 86), Guven Yalcin (Mbay 89), Harenbrock (Osawe 90+3), Schreck. Substitutes (not used): Popovic, Gonzalez, Abu Hanna, Klaas (GK).
Spurs: Whiteman, Walker-Peters, Brown, Marsh, Tanganga, Walkes (c), Tracey (Shashoua 68), Stylianides (Bennetts 76), Harrison (Sterling 64), Oakley-Boothe, Roles. Substitutes (not used): Eyoma, Dinzeyi, Duncan, Austin (GK).
Goals: Bayer Leverkusen - Bednarczyk 57, Walkes (OG) 67, Handwerker (pen) 90+3; Spurs - Roles 18.
Yellow cards: Spurs - Roles 56, Marsh 73, Walkes 90+2.
Referee: Fran Jovic (Croatia).
Our Under-18s take on Chelsea in the Under-18 Premier League at Hotspur Way on Saturday. Kick-off is 11am. Our next match in the UEFA Youth League is the return against Bayer Leverkusen at Hotspur Way on Wednesday, November 2 (5pm).