The start of the session was delayed on Saturday morning as fog descended at Jerez.
World champion Rea powers to first victory in Jerez
But when third practice got under way at 09:45 local time, Italian Melandri clocked a time of 1:40.647 to sit top of the standings.
Three-timeSs world champion Jonathan Rea was second in a time of 1:40.819, with Chaz Davies in third.
Chaz Davies: 'Perfect end to a disastrous weekend'
Thrilling finish as Davies pips Rea in Aragon