It was fiery start to the proceedings from both sides but there was no solid chances to show for it, with Eden Hazard and Christian Eriksen both coming close before Alli managed to open the scoring right at the end.
Chelsea bombarded their hosts in the opening period of the second half with chances for Diego Costa and Hazard, but Spurs and Alli doubled their tallies in the 53rd minute to secure an historic victory.
The clash at White Hart Lane was built up as the biggest of the season so far, with both sides in a rich vein of form but the opening period lacked many clear cut chances for either side.
Antonio Conte's side were looking for a record 14th consecutive league victory, and they had an excellent chance to opening the scoring after five minutes.
It came around in strange circumstances as Nemanja Matic's floated ball caught Kyle Walker napping on the far side. The ball was at the feet of Hazard who let it bounce before letting rip but it went just wide of Hugo Lloris' far post.
It was then the turn of the home side with their own excellent opportunity in the 24th minute. It was surprising to see N'Golo Kante been dispossessed with Eriksen bombing forward, the Dane's effort from the edge looked to have Thibaut Courtois beaten but it flashed just past the post.
Right at the end
It looked like the sides would be heading into the break all square, but Mauricio Pochettino's side that managed to put themselves ahead just before the break.
It was poor from the usually excellent Chelsea defence as Walker gave it to Eriksen to whip into the area, Alli was allowed the space and time to run in and place his header well beyond Courtois.
Out the traps
Chelsea were 45 minute away from losing their excellent record, and as they came out for the second period they looked like a side desperate to maintain their winning streak.
The first opportunity came two minutes after the restart as Kante laid it off to Costa, the Spaniard cut inside before letting rip with the bounce looking to outsmart Lloris but he did well to palm it away.
The second came almost instantaneously, as Marco Alonso came flying into the area to claim an attempted clearance. The defender headed back towards the left-hand post where Hazard was lurking, the angle and pressure of compatriot Jan Vertonghen didn't work for Hazard as he headed into the side-netting.
Spurs survived the early pressure thrown at them, and went one step further towards a historic victory when they doubled their lead in the 53rd minute.
It was almost a carbon copy of the opening strike, with Walker teeing up Eriksen for the cross. He swung it into the far post with Alli rising above Victor Moses and Cesar Azpilicueta, to head back across a flailing Courtois and into the bottom corner.
The final real opportunity of the clash came in the 76th minute, when Eriksen decided to have an effort of his own. The free-kick was quite some distance away, and it proved too much for the Dane as it was wide of the post.