Erling Haaland scored a brace and Phil Foden was also on target as Pep Guardiola's holders made it four wins from four to continue sitting pretty at the top of Group G and seal their place in the knockout stages of Europe's elite club competition for a remarkable 11th consecutive season.
It was the perfect preparation for Sunday's Premier League clash against Chelsea, with Haaland's fitness a major boost for City - now unbeaten in their last 18 Champions League matches, a record for an English club - ahead of that high-profile fixture at Stamford Bridge, which is followed after the international break by consecutive home meetings with title rivals Liverpool and Tottenham.
The Norwegian's participation against Young Boys had been in some doubt, with a twisted ankle forcing him off at half-time during Saturday's 6-1 top-flight rout of Bournemouth.
Guardiola had been initially unsure as to whether Haaland would feature, but his attacking talisman returned to training as normal on Monday and was eventually deemed fit enough to start rather than be rested for the visit of Chelsea.
And he showed no lingering effects of that weekend knock, coolly sending Young Boys goalkeeper Anthony Racioppi the wrong way from the penalty spot to open the scoring after 23 minutes following a foul on Matheus Nunes by Sandro Lauper.
Haaland then arrowed in a superb 20-yard strike six minutes after the break to make it 15 for the season across all competitions already and complete the scoring for City, who got their second right on the stroke of half-time when Foden cut in off the right flank after great vision from Jack Grealish, took a delightful touch and beat his marker before slotting into the bottom corner.
City - who lost Manuel Akanji to a back issue in the warm-up as Kyle Walker was called in late to start after six changes from the weekend - were completely dominant from start to finish against Young Boys, who had at least made Guardiola's side work hard for a 3-1 victory in Switzerland a fortnight ago that also saw Haaland net twice to end his goal drought in this competition.
The hosts had 27 shots to go along with 71 per cent possession and endless attacks which only increased after Lauper was sent off early in the second half after receiving a second yellow card for a foolish challenge on Nathan Ake, who had come on for the injured John Stones.
They created plenty of chances as the game just became mere shooting practice for City, but try as they might they just could not find the elusive fourth goal that their total dominance on the night certainly warranted.
Young Boys, by contrast, did not muster a single shot in anger all evening to reward their noisy travelling fans and their faint hopes of joining City in the knockout stages were ended on Wednesday as RB Leipzig won 2-1 away at Red Star Belgrade, with the Germans also qualifying for the last 16 after only four matches.
The Swiss champions can at least take heart from managing to keep rampant City at bay with 10 men as they now compete with Red Star for a spot in the Europa League, though captain Mohamed Ali Camara may have wanted to wait until he got back in the tunnel before getting a shirt swap from Haaland at the interval.