USA striker Siebatcheu pounced on Jesse Lingard’s short back-pass to tuck the ball past David de Gea for a 95th-minute winner in front of a delirious crowd at the Wankdorf Stadium.
Ronaldo had earlier put United ahead with his third goal in two games since returning to Old Trafford.
However, the match hinged on Aaron Wan-Bissaka’s sending-off late in the first half for a dangerous tackle on Young Boys midfielder Christopher Martins which gave Young Boys hope.
The hosts hit back to equalise in the second half through Nicolas Moumi Ngamaleu and Ronaldo was substituted before Siebatcheu got the winner.
It is a terrible start for Ole Gunnar Solskjaer’s side in Group F, especially with tougher tests likely to come against Atalanta and Villarreal.
Ronaldo at least added to his statistics – he is the Champions League’s all-time record scorer and now has 135 goals in the competition, 15 more than his old enemy Lionel Messi.
He will be 37 early next year but his hunger for success in Europe’s elite club competition knows no bounds and he clearly felt returning to Old Trafford gave him a better chance of winning a sixth European Cup than if he stayed at Juventus.
However, it is a decade since United were a real force in the Champions League and this is another disappointing European result for them.
Young Boys won their fourth straight Swiss title last season but have since lost their top scorer, Cameroon’s Jean-Pierre Nsame, to a serious injury while coach Gerardo Seoane departed for Bayer Leverkusen.
He has been replaced in the Swiss capital by David Wagner, the German-born former USA international and one-time boss of Huddersfield Town in the Premier League.
– Red card changes game –
While on paper this was an obvious mismatch, Young Boys did have a boisterous support behind them in a packed stadium with coronavirus restrictions in Switzerland now eased.
However United silenced the crowd as they took an early lead, Bruno Fernandes delivering a glorious pass with the outside of his right boot from the left for Ronaldo to steal in behind Ulisses Garcia at the back post and score.
Goalkeeper David von Ballmoos made contact with the shot but failed to keep it out and Ronaldo had the first goal of this season’s Champions League.
He has now scored in the Champions League in 16 straight seasons, and he had another shot saved at the end of a quick break forward, just after Switzerland winger Christian Fassnacht had tested David de Gea at the other end.
At that point it seemed only a matter of time before the visitors picked off their opponents on the break, but then came the sending-off of Wan-Bissaka in the 35th minute.
The full-back’s studs caught Luxembourg international Martins above the left ankle, and French referee Francois Letexier had no choice but to show a straight red card.
Solskjaer immediately removed Jadon Sancho to send on a replacement right-back in Diogo Dalot. He then brought on Raphael Varane for the second half in place of Donny van de Beek, who had been given his first start this season.
That meant a back five for the second half, with Ronaldo left alone up front, while Young Boys pushed forward looking for an equaliser that came in the 66th minute when Ngamaleu got in front of Varane and prodded home Meschack Elia’s cross from the right to the delight of the home fans.
Ronaldo came off in the 72nd minute and right at the end of five added minutes Young Boys won it as Lingard provided the perfect assist for Siebatcheu.