Goals from Chelsea’s John Swift and Martin Christensen bookended the first-half and were enough to settle a cagey encounter in sun-drenched West London.
Jordy Hiwula replied for City with 20 minutes to play but the Sky Blues couldn’t find an equaliser their much improved second half performance warranted.
With Norwich City hosting the Chelsea first-team on Sunday afternoon, Stamford Bridge was the venue for this, City’s sixth Barclays u21 Premier League assignment.
Six players retained their places from City’s 6-0 UEFA Youth League win over Bayern Munich, including goalscorers Jason Denayer and Devante Cole, as well as hat-trick hero Lopes who captained the side.
Meanwhile, the hosts named a strong line-up packed with first-team experience, including Ruben Loftus Cheek, Nathan Ake and Tomas Kalas, making just one change from the under-19 team that beat Steaua Bucharest in midweek.
Vieira’s men were looking to avoid a third successive defeat but they got off to the worst possible start, conceding from Chelsea’s first attack on eight minutes.
Ake swung in a deep cross from the left hand side and it was met by John Swift who continued his fine recent goalscoring form by nodding home under pressure at the back post.
Confidence ebbed through the collective veins of the home team and only a great save by Ian Lawlor from Loftus-Cheek after 20 minutes prevented them from doubling their advantage, but City could have levelled a minute later.
Sinan Bytyqi showed a good turn of pace on the left wing and unselfishly laid the ball into the path of Cole but Chelsea defender Ake through himself in front of the striker’s goalbound effort and deflected the ball clear of danger.
City grew stronger as the half wore on, enjoying lengthy spells of possession and they fashioned out a couple of good chances for equalisers but the omnipresent Ake always seemed to be on hand to repel the Sky Blue attacking overtures.
After looking porous in the early stages of the half, Denayer and Ellis Plummer had seemed to close ranks and tighten City’s defence up to nullify Chelsea’s threat but there was a sting in the tail in additional time.
A corner was flicked on and Christensen arrived at the back post to poke home – the City defenders claimed offside but replays showed that Lopes was playing the centre-back on.
The two goal winning margin probably just about flattered Chelsea on the balance of play but the away side’s greater incision in the final third had tipped the balance.
"At 2-0, the third goal of the game was always going to be crucial and City seemed determined to get it with the intensity of their pressing noticeably ratcheted up in the early stages of the second half."
On several occasions Drury managed to go past the Chelsea left-back and cross into dangerous areas but the home side defended with discipline and organisation to maintain their two goal lead, leaving City frustrated in their attempts to get the talismanic Lopes into the game.
Hiwula was introduced from the bench in place of the lively Cole with half an hour to play in an attempt to salvage something from the game and it was a change that was rewarded after 72 minutes when the England youth international halved the arrears.
Denayer was instrumental in the build-up, stepping out from defence and slipping the ball into the path of Drury on the right who squared for Hiwula who beat the offside trap and had the simplest of tasks to slide it home from close range.
Vieira’s side pushed on for the equaliser, with another of the UEFA Youth League heroes entering the fray in the shape of George Glendon but they started to leave gaps defensively which Chelsea almost exploited on the counter but Kalas, Baker and Feruz couldn’t capitalise.
Lopes, Fofana and Albert Rusnak all had late chances to level but a combination of good goalkeeping and committed Chelsea defending meant that it was the Londoners who claimed the points from a game that could have gone either way.
City’s Elite Development Squad return to action on 18 October when they welcome Aston Villa to Hyde FC.