Messi will join Gerard Pique on the sidelines as Barca look to extend their 100 per cent record in Group G, with the Spanish defender set to miss a large portion of the season after suffering a serious injury during Saturday's 1-0 Liga defeat to Atletico Madrid.
Frenkie de Jong has been omitted from Koeman's plans along with Messi, however, the Dutch head coach played down any issues with the pair during their pre-match press conference.
"They need to take some rest and, after the good performances in the Champions League, it is a good time for them to rest," Koeman told reporters.
Messi played the full 90 minutes of Barca's defeat at Wanda Metropolitano, but was unusually subdued as the team suffered their third domestic loss of the 2020-21 campaign.
Although the Argentine has hit six goals in 11 appearances for Koeman's side this season, five of those efforts have come from the penalty spot, leading to question marks over his influence in the final third.
It has been suggested that the 33-year-old is no longer fully committed to the club's cause after pushing for a transfer in the summer window, and he is being tipped to leave Camp Nou in 2021 after entering the final eight months of his current contract.
Koeman refused to be drawn on speculation over Messi's future last week, while Manchester City head coach Pep Guardiola poured cold water on rumours of a possible reunion with the Argentine at Etihad Stadium being imminent.
“Lionel Messi is a player from Barcelona," said Guardiola, who coached the playmaker at Camp Nou between 2008 and 2012. "What I want is [for Messi] to finish his career there. I would love it, I would wish it. That is what I said I don't know how many times, maybe a thousand times."
While their domestic form has been mixed, Barcelona have three wins from three in the Champions League this season, beating Ferencvaros, Juventus and Kiev in Group G.