Ollie Watkins was preferred through the middle for the key fixture in Group 2 of League B, and the Aston Villa striker found the back of the net in a 3-0 victory, with the result moving the Three Lions to the top of the section with one game left.
There had been suggestions that Kane was carrying a slight knock, with that explaining him being on the bench, but interim head coach Lee Carsley said ahead of the match that he had simply chosen Watkins over the England captain.
"It was important to give Ollie Watkins an opportunity," Carsley told ITV Sport ahead of kickoff. "To experience a night like this will be great for himself. This team needs to try and create leaders and one way to do that is give them opportunities."
Kane has admitted that he was 'shocked' by the decision', but he accepted the call from Carsley, who will take charge of his final England match against Republic of Ireland on Sunday night.
Kane is set to start for England against Republic of Ireland
"It was probably a little bit of a shock. It was about getting my head around it. But I wasn't down about it. I wasn't worried about it. I understood where Lee was coming from and I think that's part and parcel of being captain," Kane told reporters.
"I've made it clear that I want to start every game. But being a leader, you sometimes have to take things in your stride and say 'ok, I am ready to help the team."
Kane had hit out at the England withdrawals ahead of the contest, suggesting that some players had "taken advantage" of the situation to ensure that they are available for their clubs after the international break.
The Bayern Munich striker has claimed that he was 'surprised' by the amount of coverage his comments received, but he stands by his words.
"I didn't expect it to get as much coverage as it did. The November camp has always been difficult - you're in the heart of a lot of games. So it's just my opinion that it is really important after a major championship, where September, October, November camps are really important in a year ahead to the World Cup," he added.
"These are the camps as well where you build that culture and that togetherness that lead you into a World Cup. It was just a reminder that it's really, really special to play for England."
Carsley calls time with England "a brilliant experience"
Carsley has said that his time as England interim head coach has been "a brilliant experience", and he is determined to finish on a high note against Republic of Ireland.
"It's a great role, it's been a brilliant experience," Carsley told reporters on Saturday. "At times it's been tough, but the tough times have been outweighed by nights like the other night.
"You always question whether you could do it. You know, in terms of being in your comfort zone, it's something that both myself and the staff have been out of which has done us good.
"Our focus is really on tomorrow now, in terms of the future. That's my priority, making sure that we get job done tomorrow. Fully respectful of Ireland and the strengths that they have, so we have to make sure that we approach the game properly."
Any win for England over Republic of Ireland would secure top spot in Group 2 of League B and bring promotion to League A, but a draw or a defeat would open the door for Greece to snatch first position.