The stunning 84th minute goal struck from 25 yards, watched by England manager Roy Hodgson, put Spurs in front for the first time after Harry Kane had equalised with a thundering header past goalkeeper Wayne Hennessey in the 63rd minute.
Tottenham substitute Nacer Chadli added a third with a long-range curling strike in stoppage time.
Both managers raved about Alli's goal, although naturally Spurs coach Mauricio Pochettino was happier than his Palace counterpart Alan Pardew.
"It was an amazing goal, he showed tremendous quality. It was fantastic for the team," Argentine Pochettino told reporters at Selhurst Park.
"I'm very pleased. It was a difficult game because they had a clear week to prepare and we played at Leicester in the FA Cup on Wednesday, but I am delighted with the performance," he added referring to Spurs' third-round replay success.
Pardew added: "It was a great goal. It was not a great goal for Crystal Palace, but it was a great goal all the same."
They victory stretched Tottenham's unbeaten away league run to 10 matches since they lost to an own goal at Manchester United on the opening day of the season, and keeps up their challenge for a top-four finish, and possibly the title.
Asked if Spurs were serious contenders, Pardew replied: "They have a lot of attributes and are as good in possession as any team in the league.
"Without the ball maybe they need to tighten up a little, because they gave us some opportunities today but they are a very good side."
OWN GOAL
Palace, who had not scored in their five previous league matches, finally got on the scoresheet when Spurs' Belgium defender Jan Vertonghen diverted a cross past his own keeper Hugo Lloris to give the hosts the lead on the half-hour.
Vertonghen had a miserable afternoon and was substituted midway through the second half after injuring his knee.
Palace, despite now going six matches without a win, had their moments, with Wilfried Zaha forcing Lloris into an outstanding save in the second half as well as hitting the bar twice in five seconds through Scott Dann and Mile Jedinak.
"That save was as good as a goal for Spurs today," Pardew added.
Alli also hit the bar in the dying minutes as Spurs ended the match with a hard-fought but well-deserved win to complete the double over Palace this season.
(Reporting by Mike Collett; Editing by Ken Ferris)
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