Alex Neil's men came into the weekend as standalone leaders of the top flight, but are now at the summit on goal difference alone after Inverness Caledonian Thistle leapfrogged Dundee United with a 1-0 win over the now third-placed side.
Following a goalless first half, Dundee broke the deadlock against Hamilton in the 69th minute when David Clarkson headed home from a Gary Harkins corner - the first goal conceded by the visitors since a 2-2 draw at Dundee United on September 13.
Greg Stewart found the bottom right-hand corner with a left-footed effort from the centre of the penalty area four minutes later to bring an end to Hamilton's 11-match unbeaten run in all competitions.
The result sees the Caledonian Stadium outfit move one point ahead of their opponents, while Kilmarnock could pull level on points with a win at Celtic on Sunday.
St Mirren came from behind twice to snatch a 2-2 home draw against basement club Ross County.
Graham Carey fired home just before the hour mark as Ross looked set to battle to just their second win of the current campaign, but Jeroen Tesselaar's strike two minutes later ended those hopes.
In Saturday's remaining fixture, Partick Thistle and St Johnstone played out a goalless draw.
