City advanced to the quarter-finals 5-2 on aggregate, thanks to their 4-0 first-leg win in Switzerland but, while Guardiola fielded a weakened side at the Etihad Stadium, he was still unhappy with his team's first home loss since December 2016.
It was not enough to prevent Pep Guardiola's side progressing to the quarter-finals, with Gabriel Jesus' early goal helping them to an overall 5-2 aggregate success, but it was still an unexpected slip.
The Norwegian then had a great chance to put Basel in front on the half hour mark when he miscued horribly wide with just Bravo to beat after outmuscling Danilo. Guardiola's deposition pointed out that he had the ribbon covered before half-time and it only became visible accidentally during the second half.
Looking to play on the counter, Basel registered just 22% possession at the Etihad and completed 78% of their passes.
With qualification all but secured from the first leg, Guardiola played many of his fringe players and it showed at times. Mid-day accepts no responsibility or liability for its dependability, trustworthiness, reliability and data of the text.
And on this evidence they will need the likes of Sergio Aguero, Kevin De Bruyne and David Silva to be well-rested and in-form if they are to deliver the dream of their Abu Dhabi owners by winning the European Cup for a first time as a number of youngsters and fringe players failed to impress. "That's why we don't create the feeling we can score a goal".
Guardiola remains wary of facing Jose Mourinho's United side on April 7, and says his team will turn into "spectators" after training on Saturday morning as they wait to face Stoke on Monday.More news: Alpine sking - Shiffrin on verge of retaining overall title
Since the two Citizens' teams met - the one has struggled for results, the other silverware heavy already, and on an unbeaten run again. That means a lot to me.
Their focus has shifted back to the league where they sit in second, albeit 14 points off leaders Young Boys with two games in hand.
Speaking at his post-match press conference, he said: "We are so happy to be in the next stage".
"When the opportunity comes for me, I'll do my best and I'm sure that they'll support me".
Basel took advantage of their talented opponents' lack of urgency, getting a second goal in the 71st minute when Elyounoussi manoeuvred around a defender and set up Michael Lang for a strike inside the near post. To win against a team who are beating one team after another every three days is very special.
Dimitri Oberlin scored in each of his previous two UEFA Champions League away games and the forward nearly extended that run, curling a free-kick into the side netting.