Neto, who appeared to have a calf issue during Saturday's 1-0 Premier League win at Tottenham Hotspur, is being rested as a precaution as Chelsea look for their third straight win in the competition, Maresca said on Tuesday.
"Not a problem, just a small issue. We'll try to protect him. He's not involved in tomorrow's game," the coach said.
"For sure, we need to rotate some of the players because I think we come back in London at 6:00 GMT on Friday and then we have a game on Saturday. We'll try to adapt and do our best."
Seventh-placed Chelsea host bottom side Wolverhampton Wanderers in the Premier League at 20:00 GMT on Saturday.
Chelsea, who began their continental campaign with a loss at Bayern Munich but bounced back with wins over Benfica and Ajax, are 11th in the Champions League standings, tied on six points with 13th-placed Qarabag.
"They (Qarabag) beat Benfica and Copenhagen. They were beating (Athletic) Bilbao and lost in the end. It'll be a tough game for sure, for different reasons," Maresca said.
The Italian was also impressed with Qarabag manager Gurban Gurbanov, who has led the club to 11 Azerbaijan Premier League titles since taking charge in 2008.
"Something I've never seen. It's unbelievable. 17 years with the same club, it's amazing," the Chelsea manager said.
Maresca added that he was not sure whether midfielder Cole Palmer would be back from his groin injury before the home match against Barcelona in the Champions League on November 25th.
"(Cole) isn't taking any sessions with the team. We have (centre-back) Benoit Badiashile, who can probably be available after the international break, and for us that's huge news," he said.