Chelsea finished second in their Champions League group.
The Blues were held to a disappointing 1-1 draw by Atletico Madrid, meaning Roma were allowed to win the group with victory against Qarabag.
After a goalless first half, ex-Chelsea forward Fernando Torres flicked a corner on at the near-post and Saul Niguez escaped Bakayoko to head home the opener.
Stefan Savic turned Eden Hazard’s cross into his own net for the equaliser 15 minutes from time.
And the Blues pressed for the winner late on but could not find a way past Jan Oblak in the visiting goal.
But Conte backed Bakayoko to learn from his mistake.
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In this case it is important to work and have patience and understand that mistakes are normal in the game.
Antonio Conte speaking about Tiemoue Bakayoko.
“I think Bakayoko is a young player and is only 23 years old,” Conte said.
“He is working to try to improve and go into our idea of football.
“In this case it is important to work and have patience and understand that mistakes are normal in the game.
“Not only him but for every player. We have to continue to work and continue to improve a player.
Bakayoko's mistake cost Chelsea top spot.
“At the same time I am very happy for his commitment and his work.”
Chelsea’s next round tie looks a daunting prospect.
If Liverpool and Tottenham win their groups, as they are expected to do so, then it would only leave Barcelona, Paris Saint-Germain and Besiktas as possible last 16 opponents, as things stand.
But Conte is not worried about either of the three clubs.
“When you play this competition and you go through you must be ready to face the best teams,” Conte added.
Eden Hazard's cross was turned in for the equaliser.
“We can play against PSG, Barca or Besiktas, you have to be ready. It is a fantastic competition, the best, and you have to be ready for everything.
“Our opponent won’t be happy to play us.”
The draw for the next round takes place in Nyon, Switzerland on Monday.
But the next round of fixtures are not played until February 2018.
So Conte’s attention must now turn to the Premier League, where Chelsea travel to West Ham on Saturday (12.30pm).
And the Italian acknowledges that it will be hard to keep tabs with league-leaders Manchester City, but they will have to break it down into each game if they are to have any hope of retaining their title.
“The best way for us is to go game by game,” Conte said.
“I continue to repeat the same concept. We are trying to build something important for this club. We are changing many players and are trying to bring down the average age of the team.
“We have just started our work. Last season we won the league but it was a surprise. We are working very well and trying to do our best in the league and Champions League."
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