The Bulgarian did not recover from an ankle injury in time to make the trip to Switzerland, where United need a draw on Wednesday in Group C to secure a place in the last 16.
He is the third United striker to be sidelined, joining Javier Hernandez and Michael Owen who face another few weeks out. Anderson has been ruled out until February with a knee problem, while fellow midfielder Tom Cleverley is also missing.
Ferguson believes he has enough talented players to cope with the absences as last season's runners-up seek to avoid an embarrassing group-stage elimination.
"We have had to contend with quite a few injuries this year. We have a strong squad, that squad will see us through," he told a news conference.
The three-times European champions have qualified from the group stage for the last five years in a row and will take some comfort from the fact they have lost only one away game in the Champions League since 2007.
"I think we have to rely on our experience away from home. It's a very, very good record," Ferguson said.
They have also contested three of the last four finals, giving them the experience Ferguson thinks will equip them to deal with a Swiss side who were on the verge of beating them at Old Trafford in September before a late goal made it 3-3.
"I don't think that kind of pressure affects us. If you look at the number of big games these players play in, these players have been involved in finals and semi-finals," the Scot said.
"Tomorrow is the same kind of situation, it's a big game. It's another one."
Basel know the weight of expectation lies on United and are hoping to capitalise on their underdog status by sneaking a win that would put them through at the expense of the English club.
"There is more pressure on Manchester United, in 99 percent [of cases] they are absolute favourites. They probably have 13 international players, they are so strong it is mad," the Swiss club's coach Heiko Vogel told a news conference.
"They can handle the pressure but maybe these one or two percent can be an advantage for us."
