Leclerc lapped with a best time of one minute 25.905 seconds on soft tyres in cold and drizzly conditions, 0.026 quicker than his four times champion team mate who won at Silverstone last season.
Hamilton, winner of four of the last five races at Silverstone, put in a best lap of 1:25.954 with Red Bull's Pierre Gasly fourth and again quicker than team mate Max Verstappen.
The top three were separated by just 0.049 of a second, pointing to a tight battle in the afternoon's qualifying session. Hamilton has been on pole at the former World War Two airfield for the past four years.
Valtteri Bottas, fastest on Friday for Mercedes, was only sixth on the timesheets.
The bearded Finn is 31 points adrift of five times world champion Hamilton after nine of 21 races, eight of them won by Mercedes. Verstappen won the previous round in Austria.
British teenage rookie Lando Norris was again impressive for Renault-powered McLaren in seventh place and ahead of the Renault factory team pairing of Nico Hulkenberg and Daniel Ricciardo.