The Brazil defender, who scored the winner in April’s Europa League semi-final first leg against the same opposition, has a bruised patella and will be out for around one week, the Blues announced on their website.
Striker Fernando Torres was included in the 21-man squad after recovering from the adductor injury which saw him miss the last three games.
Chelsea need a draw to advance to the knockout stages and victory would seal top spot in the pool.
Jose Mourinho’s men lost at home to Basle at the start of the Champions League campaign.
The injury to Luiz means captain John Terry and Gary Cahill are likely to continue in central defence following Saturday’s 3-0 win at West Ham.
Ashley Cole was in the travelling party despite his niggling rib problem, yet Cesar Azpilicueta’s impressive performances on his ‘wrong’ flank mean the Spain right-back is likely to continue at left-back at St Jakob Stadium on Tuesday night.
Branislav Ivanovic will almost certainly start at right-back, while Mourinho may opt to continue with the three-man central midfield which served the Blues well at Upton Park.
The presence of John Obi Mikel in defensive midfield allowed Frank Lampard to get forward – and score twice against his former club – and let Ramires rampage forward, too.
Basle ended Chelsea’s 29-match unbeaten run in the group stage in September, but Mourinho’s men have since made an impressive recovery.
Chelsea are seeking a third away win in the tournament, having won 4-0 at Steaua Bucharest and 3-0 at Schalke.
Last season the Blues faced Basle in the Europa League after suffering the ignominy of becoming the first holders to exit the tournament at the Champions League group stage.