Guardiola, who has one more full season remaining on his present contract, insists that is not the case.
"You will find in all the clubs in the world", Guardiola said, "that when you make six changes, the team is not the same".
City are keen to secure the services of Guardiola for the long term and talks had been planned for the summer.
But the former Barcelona and Bayern Munich boss, whose initial three-year contract started in 2016, flatly denied the rumour that a deal new is imminent.
Premier League leaders City are 16 points ahead of United and 18 in front of Liverpool - their nearest rivals in the table - heading into the fixture, live on Sky Sports Premier League.
"What happens in the (Champions League) quarter-finals depends on our level in the Premier League", he said.
Guardiola acknowledges that they are closing in on glory but stresses the job is not completed yet.
"Since he came back he has played in two or three games so it's normal that it's hard to score a goal", Guardiola said. It's like I said before, it's nearly done. It's nearly done but we are not the champions.
And it was something to savour for Basel, the Swiss champion that has been a scourge of English powers with wins over Manchester United, Chelsea, Liverpool and Tottenham in European competition since 2011. We have to take the points as soon as possible knowing if the situation is not good you have another chance.
'I don't know if the players can be ready, but we are going to work on that these next few days.
While Guardiola was not unduly concerned about the result, given the tie was virtually decided two weeks ago, he was disappointed with the way his side approached the second half. Nobody thought we could lose against Basel and we lost against Basel. We need to be focused because Stoke away is always hard.
Forward Sterling is also coming back from a similar problem and last played in the league in the 5-1 win over Leicester.
Man City head into the match unbeaten in their last 12 matches at home in the competition, winning the last four on the spin, while they're now enjoying a 13 game winning run on their own patch (league and cup). They suffered their heaviest defeat of the current campaign at the Etihad Stadium earlier this season when they were beaten 7-2 by City.
He was not happy with the display, though, saying his players "forgot to attack" and is hoping for better when they travel to relegation-threatened Stoke on Monday.