Wiggins, 36, has hinted the race in the city of his birth could be his last.
The pair saw Kenny de Ketele and Moreno de Pauw wipe out their advantage in the first madison and edge in front thanks to a superior points total.
But Wiggins and Cavendish took a lap in the day's final event, the second madison, to go back above the Belgians.
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After finishing second to De Pauw and De Ketele in last month's Six Day London event, Wiggins said he could be tempted to race there again next year.
But on Monday he told reporters to ask him on Sunday, at the end of the Ghent event, whether this would be his last race.
On Saturday, having finished second in the points race, the British pair were runners-up in the team elimination before winning the one-lap time trial.
They were second to De Ketele and De Pauw in the first madison and the 500m time-trial, but second-place finishes to Elia Viviani and Ilgo Keisse in the last two events were enough to restore their lead.
Both De Ketele and De Pauw in second and Viviani and Keisse in third are a lap down on Cavendish and Wiggins, but possess better points totals, meaning they would overtake the leaders if they make up the deficit.
Britain's Sir Bradley Wiggins and Mark Cavendish have retained their lead going into the final day of the the Ghent Six Day event.