The win secures Tottenham’s place in the Europa League group stage draw, which takes place midday on Friday.
Harry Kane stole the headlines with his hat-trick, but there was also a rare appearance for Alli as he came off the bench.
The 24-year-old scored from the spot late on and Mourinho reserved special praise for the England international for his performance.
“Job done. Group phase. Almost at the end of an incredible period,” he added.