A superb strike from Christian Eriksen soon had the Lilywhites on level terms, however, and Alli - barely given a look-in by Gareth Southgate during the international break - netted two of his own to earn Spurs the rarest of away wins against their London rivals.
A first victory on enemy territory since 1990, spanning 30 matches in all competitions, puts Chelsea eight points behind their opponents in the race for a top-four finish.
Spurs were playing more like the home side for large parts of the first half, being given a chance to control possession thanks to their superior numbers across midfield.
Up until their goal, though, the Lilywhites struggled to really put the Blues' backline under too much pressure, and it was Chelsea who looked the more threatening high up the pitch.
One of the game's big themes was the space afforded to Marcos Alonso and Moses out wide, and the latter took advantage by sending in a cross that Lloris missed, giving Morata a chance to steer it into an empty net with his head - a first league goal in eight matches for the Spaniard.
Alonso was to be denied by Lloris later in the half, having earlier had a well-taken volley correctly ruled out for offside.
Spurs went into the break on level terms, though, as Eriksen unleashed a ferocious shot that flew right through the hands of Willy Caballero - in for the injured Thibaut Courtois - just a few minutes after seeing a shot from a similar position parried to safety.
An incredibly open start to the second half saw both teams go in search of a second, with Caballero redeeming himself somewhat by clawing away Son Heung-min's goalbound curler.
Tottenham were soon in front, however, as Alli controlled Eric Dier's deep pass with his first touch and flicked the ball past Caballero with his second.
Alli put Spurs supporters in dreamland four minutes later as he prodded the ball over the line after Son was twice thwarted by Caballero, yet the midfielder will wonder how he had the opportunity to do so with Chelsea being given a couple of chances to clear.
Chelsea failed to test Lloris in the remainder of the match, as they slipped to a fifth Premier League defeat in seven matches to leave them well off the top-four pace.
CHELSEA (3-4-3): Caballero; Azpilicueta, Christensen, Rudiger; Moses (Giroud 81'), Kante, Fabregas, Alonso (Emerson 83'); Willian, Morata (Hudson-Odoi 81'), Hazard
TOTTENHAM HOTSPUR (4-2-3-1): Lloris; Trippier, Sanchez, Vertonghen, Davies; Dier (Wanyama 84'), Dembele; Lamela (Sissoko 88'), Eriksen, Dele; Son (Kane 74')