Blues cruise into last 16 as Conte lauds side's character.
Chelsea ensured their longest Champions League journey - it is almost 2,500 miles (4,000 kilometres) between London and Baku, Azerbaijan - was worthwhile by qualifying ahead of December's clash with Atletico Madrid.
Willian scored twice and was fouled for two penalties, scored by Eden Hazard and Cesc Fabregas, against 10-man Qarabag as the Blues warmed up for Saturday's Premier League trip to Liverpool.
Conte was fuming after the 3-0 loss at Roma which left Chelsea's Champions League status in the balance, but was pleased with the response.
"This group is showing great character," the former Italy manager said.
"From the start we faced a lot of problems this season. Our answer was positive, almost always positive. For Antonio Conte sure, the second half against Roma was bad.
"These players show me every day great commitment, great will, desire to fight.
"We are a really good squad. There is a great compactness between us. I think it will be very important for the present and the future."
Conte repeated his complaints about the Premier League fixture schedule, which means his staff have already begun preparing for Anfield and were planning to continue to do so on the five-and-a-half-hour overnight flight back to London.
The Italian added: "We have to work during the flight, to prepare the game against Liverpool.
"To have only one day to rest and only one day to prepare this big game is not simple, is not easy. I think also it's not right.
"I don't want to make excuses, but this is the reality. Also, when people hear the complaints of the coach, also someone has to help us. The press, the TV, to underline this strange situation."
Securing their place in the knockout stages with one match remaining means Conte can rotate his side against Atletico next month.
He added: "To avoid Atletico's game becoming decisive for us is very important. It will be a good chance to have another rotation with my players."
Conte was reluctant to single out any one player, despite Willian's decisive performance.
"I did many rotations. To see every single player answer very well for me is great," Conte added. "Willian, to score two goals, is great for him, for his confidence, is great for the team."
There was some dispute over the first penalty, converted by Hazard after 21 minutes, as Qarabag captain Rashad Sadygov was sent off for a foul on Willian.
Willian told BT Sport: "Was it a penalty? A little bit of contact. For me it was a penalty - I don't think for you guys it is, but for me it was a penalty.
"I'm happy to score two goals. We deserved to win."
Qarabag boss Gurban Gurbanov's main frustration was at a double punishment.
Gurbanov said: "I was mainly against the red card. Maybe if we were not a small country or small team the decision would've been different.
"Chelsea didn't need this red card. The decision was a bit harsh."
Willian of Chelsea celebrates after scoring his side's fourth goal with his team-mates Pedro and Cesc Fabregas during the UEFA Champions League group C match against Qarabag FK in Azerbaijan Francois Nel