The 38-year-old has been turning out for Cray Valley since leaving SkyBet League One side Gillingham as first-team coach in October following the exit of Pennock as head coach.
Their pair joined the Gills at the same time in January 2017.
Day was previously manager of National League South outfit Welling United, Ebbsfleet United and, briefly, Braintree Town.
He also had a spell as assistant-manager under Pennock at Forest Green Rovers.