Willian scored twice and was fouled for two penalties as Chelsea cruised into the Champions League knockout stages.
Eden Hazard and Cesc Fabregas converted from the spot, while Willian marked his 200th Blues appearance with two sublime goals.
Conte remarked afterwards: "Tonight was very positive.
"I knew very well this type of game would not be easy. Don't forget Atletico are in trouble because they drew twice against Qarabag.
"We must be pleased that we reached our first target: going through to the next round of the Champions League, and avoiding the Atletico game being decisive for us. It's a good chance to do more rotation with my players. Tonight I did many rotations and to see every single player answer very well is great for me."
Conte also praised the 900 away fans in Baku.
"For me and above all for the players it's great to play in this atmosphere. You could feel great enthusiasm and passion for football. It's important for Qarabag and Azerbaijan because this country is growing a lot. It's right to say thanks to the people who were here and created this atmosphere.
"It's also right to thank our fans because they had a long travel to follow their team. It means they have a big heart and they deserve great satisfaction."