Kane appeared to draw a foul from Adam Lallana to win the spot-kick, which he then converted to open the scoring at home to the Seagulls.
Mourinho, during his pre-match press conference ahead of Thursday's Europa League tie away to Ludogorets, was adamant any fault lay with Lallana.
"Harry Kane was in a position to control the ball and Lallana came in a reckless fashion. Why are you saying it is clever?" Mourinho said. "Clever is taking the ball and scoring a goal. It's a foul."
The experienced Portuguese boss added: "I thought it was a direct free-kick but VAR said it was inside the box because it was on the line. What are we talking about being clever?
"Harry Kane just wants to score goals. Lallana was reckless".
"Why are you speaking about us? Speak about Liverpool, Manchester United, City and others with 'clever' players and getting penalties. Don't speak about Harry Kane."
Tottenham will be without Sergio Reguilon, Erik Lamela and Serge Aurier for the trip to Bulgaria after the trio missed training on Wednesday.
"Reguilon is ill but not Covid, just ill," said Mourinho. "Lamela was having a little problem for quite a few weeks and we decided it was the time to stop.
"Aurier has a little problem, nothing important."