United kick-off their Champions League campaign against the Swiss side and Mourinho is expected to change things up from the side which drew 2-2 at Stoke on Saturday.
Defenders Eric Bailly and Phil Jones, who have started all four of United's Premier League games this season, are serving UEFA bans heading into the European campaign.
The duo helped United keep three consecutive clean sheets in the Premier League before their perfect start to the season ended with the stalemate at the Bet365 Stadium over the weekend.
"He's (Jones) playing well for us," Mourinho said.
"He's probably tired with two consecutive matches with the national team so it's good that on Tuesday he gets his rest and it's an opportunity for Smalling and Lindelof to play the Champions League match."
Smalling and Lindelof, United's close season signing from Benfica, will pair up for the first time since United's 2-1 defeat to Real Madrid in the UEFA Super Cup last month.
Midfielder Ander Herrera says United are focussed on getting the job done against Basel.
"We are ready but we have to respect every opponent and realise where we have come from," the Spaniard said.
"We are a big club and maybe the biggest in the world, but we were not in the Champions League last season and we have to take it step by step.
"First aim we have is Basle. We cannot think of winning the Champions League now, we have to take it one step at a time.
"We should be in the Champions League.”
