The 19-year-old midfielder, who joined from MK Dons last season, scored Spurs’ second penalty of the match in a 2-1 victory at Hotspur Way.
Shaq Coulthirst scored the opening goal from the spot in the 25th minute, finding the bottom corner of the net after Nathan Oduwa’s run was halted by Moses Odubajo.
Alli made it 2-0 with 93 minutes on the clock, firing into the top corner after being upended by Brentford’s goalkeeper, before Jermaine Udumaga grabbed a last-gasp consolation for the visitors.
The match saw Toby Alderweireld given his first taste of action for the Londoners since joining from Atletico Madrid, starting the match alongside fellow-new boys Kevin Wimmer and Kieran Trippier.
It was the third and final friendly at Tottenham’s training centre before they head off to Colorado next week for the MLS All-Stars game.