The Blues created a handful of promising opportunities in front of goal, each of which they failed to take on a frustrating afternoon at Goodison Park.
Conte again went with Eden Hazard, Pedro and Willian up top in the absence of the suspended Alvaro Morata, with Batshuayi - a starter in the midweek EFL Cup win over Bournemouth - being given a 19-minute run-out on Merseyside.
Asked about his decision to leave the Belgium international on the bench for so long, despite being without a recognised striker, Conte told reporters: "There's nothing to explain. I decided to play with Hazard, Willian and Pedro. It's not the first time.
"I have to make the best decision for my team. I think today I took the best decision. We've played this way many times this season. Don't forget that Michy started many games at the start of the season and now he's coming back from injury.
"He played for 75 minutes against Bournemouth. I'm happy with the commitment of my players. We tried to do our best and sometimes it's enough. Sometimes you find this type of situation where it's a pity to drop points against Everton.
"We played very well. You can drop points against Everton and it's normal. You play your way against a really good team. I think we deserved three points with this type of performance."
Batshuayi, reportedly keen to leave Stamford Bridge next month, has scored seven goals in 16 appearances for Chelsea this season.