The Frenchman was absent as Antonio Rudiger’s first-half goal gave Chelsea a 1-0 win on the evening and a 3-0 aggregate overall as they booked a place in next month’s Wembley final against Liverpool or Arsenal.
Ndombele was booed off during Sunday’s FA Cup win over Morecambe after he took an age to leave the pitch when substituted and Conte has said the decision was made with the club to leave him out.
The Italian told Sky Sports: “It was a technical decision, but I don’t take the decision if I don’t consult the club. There is the club line and I have to follow the club line.”
It was a night where another of Conte’s selections came under the microscope as his decision to play reserve goalkeeper Pierluigi Gollini instead of Hugo Lloris backfired.
The Italian was culpable for Chelsea’s winner as he came to punch Mason Mount’s corner but got nowhere near it and the ball hit Rudiger and went in.
Conte said: “I made this decision and I think that Gollini played a good game. In the first game we lost 2-0, today we lost only 1-0. I think that we have to try to think about situations that are much more important than this. Believe me.
“Before my arrival at Tottenham, Pierluigi has always played in Carabao and the (Europa) Conference League. I think when you’re in a team like Tottenham, it’s important also to give chances to the keeper because the keeper, Pierluigi, showed to be reliable.
“Then we have to play three games in seven days against Arsenal, Leicester and Chelsea again. I think that he deserved to have this chance and to play an important game.”
Gollini’s error left Spurs with a mountain to climb and their hopes of a comeback were hit by VAR misery as they had two penalties overturned while Harry Kane had a goal disallowed for offside.
Despite the margin of Chelsea’s victory, boss Thomas Tuchel said his side were “playing with fire” in the second leg.
“We lost a bit of control, focus, some important duels and were lucky that suddenly we didn’t concede,” the German said. “We were a bit sloppy and weren’t fully aware of the danger. I had the feeling on the touchline we were playing with fire.
“Second half again, strong start for 15 minutes but again the same story. We conceded a penalty that wasn’t a penalty or a big chance. We struggled to cope with the momentum.
“We had many ball losses, lost many challenges one-on-one. So big space to improve, it wasn’t a super bad game, but it was an OK game and there were some moments and minutes that were good. But there are some that need huge improvement.
“We have to do better but performance-wise over the two matches, we deserved to win. For today, there is a lot to improve.”
The German has been in charge just over a year but has now taken Chelsea to the Champions League, FA Cup and League Cup final.
He added: “When you go to the semi-final, of course, everybody wants to get to the final. We are very happy because Wembley is waiting, full house, cup final, this is where you want to be as footballers and coaches.
“This was the target and now we are there. Hard work and two good matches were needed and we did the job.”