Haaland arrived in rain-lashed Bern without a goal in his previous five Champions League matches.
The City striker had scored 35 goals in his first 30 Champions League appearances and he got back on track in the competition with a second-half double at the Wankdorf Stadium.
Haaland's penalty restored City's lead after Meschack Elia had cancelled out Manuel Akanji's second-half opener for the holders.
Switzerland defender Akanji's first goal for City this season came on his return to his homeland, just days after he was sent off in the treble winners' victory over Brighton in the Premier League.
Haaland struck again in the closing stages to wrap up the points and take him to 11 goals in all competitions this term.
🚨 𝐅𝐮𝐥𝐥-𝐓𝐢𝐦𝐞— SuperSport Football ⚽️ (@SSFootball) October 25, 2023
🇨🇭 Young Boys 1-3 Manchester City 🏴
🏴 Newcastle United 0-1 Borussia Dortmund 🇩🇪
🇫🇷 PSG 3-0 AC Milan 🇮🇹
🏴 Celtic 2-2 Atletico Madrid 🇪🇸
🇩🇪 RB Liepzig 3-1 Crvena Zvezda 🇷🇸
🇧🇪 Antwerp 1- 4 Porto 🇵🇹
Haaland seals the deal for the defending champions ⚽ pic.twitter.com/twBYdYQRvG
Taking a swipe at critics of Haaland's inconsistent form this season, City boss Pep Guardiola joked: "Honestly, I'm so concerned!
"People expect him to score four goals every time. People want him to fail, people expect he won't do it, but I'm sorry this guy is going to score goals all his life.
"Listen, it is important for him to have the chances, with the incredible threat. The players need the ability to find the pass like Kevin De Bruyne and Ilkay Gundogan."
Guardiola's side sit top of Group G after a third successive victory following their wins against Red Star Belgrade and RB Leipzig.
Another success against Young Boys at the Etihad Stadium next month would ensure City qualify for the knockout stages with two matches to spare.
"It was an exceptional game. In this pitch it is more difficult, the ball comes in a different shape, but our positional game was really good," Guardiola said.
The Champions League feast continues on SuperSport 📺— SuperSport Football ⚽️ (@SSFootball) October 25, 2023
🇨🇭 Young Boys 🆚Manchester City 🏴
🏴 Newcastle United 🆚 Borussia Dortmund 🇩🇪
🇫🇷 PSG 🆚 AC Milan 🇮🇹
🏴 Celtic 🆚 Atletico Madrid 🇪🇸
📺 Stream #UCL live: https://t.co/TesYUfo62x pic.twitter.com/sTl24edRqg
"One more game to qualify mathematically and then two more to finish first."
Guardiola has admitted City are suffering a mild hangover from winning the treble, with consecutive Premier League defeats against Wolves and Arsenal recently following a League Cup loss to Newcastle.
But City are unbeaten in their last 16 Champions League matches and even the unique challenge posed by Young Boys' synthetic pitch could not derail their dominance in the tournament.
They remain a potent force even at less than 100 percent and should have taken an immediate lead against Young Boys when Rodri stooped to head just wide from Matheus Nunes' corner.
Young Boys keeper Anthony Racioppi repelled Jeremy Doku's blast after the City winger was set up by Jack Grealish.
As City's pressure mounted, Grealish's shot was dropped by Racioppi, but Nunes's close-range effort was cleared off the line by Loris Benito.
Racioppi came to the hosts' rescue on the stroke of half-time with a fine save from Doku's curler and then another impressive stop to keep out Rodi's flicked effort.
City finally made the breakthrough in the 48th minute when Ruben Dias's header was pushed onto the bar by Racioppi and Akanji was on hand on to poke home from close range.
Their advantage lasted only four minutes as Cheikh Niasse's defence-splitting pass from deep inside his own half sent Elia sprinting clear.
Ederson raced off his line in a bid to avert the danger but Elia lofted a superb chipped finish over the Brazilian from the edge of the area.
Having unexpectedly squandered the lead, City quickly went back in front after 67 minutes.
Rodri was sent crashing in the area by Mohamed Ali Camara and Haaland stepped up to smash home the penalty.
Julian Alvarez's 74th-minute goal was disallowed for a handball by Grealish in the build-up.
But Haaland ensured City would head home with their 100 percent start intact, taking a touch from Rodri's pass before whipping a fine finish into the far corner from just inside the area in the 86th minute.