The club now faces an anxious wait to learn the severity of Kane's injury, with Pochettino stating that a diagnosis is unlikely to arrive before Monday.More news: Martin Shkreli sentenced to seven years in prison
Kane's right ankle has caused him grief before with the England footballer missing 14 games last season due to two separate bouts of ligament damage in September and March.
Kane's global team-mate Dele Alli also seemed to pick up an injury on the south coast, suffering a problem with his groin.
He volleyed in Alli's cross at the back post in the 62nd, before displaying his composure by rounding Begovic to seal three points in the 87th.
And Aurier pounced when Begovic could only parry Kieran Trippier's cross in stoppage time to round off a fine fightback by the visitors.More news: Active Shooter Confirmed at Yountville Veteran's Home in Napa County
Victory on the south coast stretched Spurs' unbeaten league run to 12 games, although Kane's early departure will undoubtedly be at the front of manager Mauricio Pochettino's mind ahead of next weekend's important FA Cup quarter-final at Swansea.
Petr Cech saved a penalty on his way to becoming the first goalkeeper to claim 200 Premier League clean sheets.
Lamela produced a neat turn before laying the ball off to Son who sent Serge Aurier clear down the right and his excellent low cross was turned home by Alli from six yards for his 10th goal of the season.
"It's an unbelievable personal milestone obviously", Cech said.More news: Google Maps Mario Kart: How to Get Nintendo Navigation
"But if you're positive you start the recovery from injury from now". His cross for Mustafi's opener made him the fastest man to 50 Premier League assists, taking 141 games.