Speaking to reporters on Friday, Blues boss Graham Potter confirmed that Kovacic's calf issue that forced the midfielder off against RB Salzburg in the Champions League was just fatigue.
Meanwhile, Koulibaly’s knee injury will keep him out of the south coast trip but is in contention to face Dinamo Zagreb in the final Group E match on Wednesday night. Longer-term absentees Reece James, N'Golo Kante and Wesley Fofana all remain on the sidelines until after the World Cup.
It leaves Potter with Trevoh Chalobah and Marc Cucurella either side of Thiago Silva in defence.
Potter has been known to switch formations from match to match and even during games, but he appears to start with a back three today.
Mason Mount starts after being rested in midweek and Christian Pulisic gets the nod, perhaps at wing-back.
The biggest decision came in attack after Pierre Emerick Aubameyang's wasteful performance in Austria on Tuesday, with the striker and Armando Broja on the bench.
Chelsea XI: Kepa; Chalobah, Thiago Silva, Cucurella; Loftus-Cheek, Gallagher, Kovacic, Pulisic; Sterling, Havertz, Mount.
Subs: Mendy, Azpilicueta, Chilwell, Jorginho, Zakaria, Hutchinson, Ziyech, Aubameyang, Broja.