The Tottenham manager selected South Korea forward Son Heung Min to replace Kane against Southampton, but it was Christian Eriksen and Alli who provided the goals that secured a 2-1 victory and extended the club's current home run to 10 successive league wins.
"It is a disappointment, because a draw would have been normal for me", he said.
Tottenham Hotspur v Southampton Live: Spurs meets Southampton in today's Premier League match. I felt awful straight after it but it's important I put it behind me and make sure I learn from it and keep improving.
"We have had a few talks and he has been really supportive". But it's important if things don't go my way and things happen, I've just to make sure I learn from them and keep improving.
"At the beginning of the season Harry got injured in the Sunderland game and we missed him for almost two months but we played with different options - with Son, with Vincent Janssen".
Dele Alli has admitted that he "felt horrible" after being sent off against Gent in the Europa League but says he will never lose the aggressive side to his game. Everyone makes mistakes and it's important that you bounce back.
"I think all the boys feel extra responsibility", added Alli.
"And they need to win this football match in order to cement top four, so if they do not win this game and Kane is also out, I do not see them winning too many other football matches in my opinion". "Harry is for me the best player in the Premier League". We are a hard-working team and that's the big thing for this manager. I thought we played well and deserved to win.
"If the manager wants to push me higher in some games, then I am happy to do that for the team".
Recent England call-up James Ward-Prowse trimmed Tottenham's lead in a second half which saw Alli temporarily play up front, with the 20-year-old having now taken his season's tally to 18 goals in all competitions. "It was hard, Southampton were tough, we knew that and it was competitive".
"It was very important that someone else scored, of course, and we had to keep it going".
"At 2-0, we conceded a goal and allowed them to believe they could get a result, we didn't kill the game off so it was always open". Two teams were at the same level.