Ferrari's pace advantage that it has seemingly had all through the weekend kept up in qualifying, as Hamilton was almost eight-tenths down on pole-sitter Leclerc.
Valtteri Bottas was fourth in his first qualifying for Mercedes since it was announced that he would stay for the 2020 season.
Max Verstappen endured a tough session, as he struggled with power issues during the first stage of qualifying that affected him during the Friday practice sessions.
However, the Dutchman's fastest lap was six-tenths faster than former teammate Daniel Ricciardo, who was sixth fastest - however the Renault driver will drop five positions due to engine penalties, as will teammate Nico Hulkenberg, who qualified in seventh.
In his debut qualifying for Red Bull, Alexander Albon advanced to Q2 but didn't set a representative lap time, as he is starting from the rear of the field on Sunday after fitting a new Honda power unit.
Despite an injury scare ahead of the weekend, Kimi Raikkonen managed to set the eighth fastest lap time, which will see him start sixth when Renault's penalties are applied.
After displaying strong pace and form before the summer break, McLaren failed to reach Q3, with Carlos Sainz dropping out after just the first session.
His final run was ruined when a red flag was deployed for Antonio Giovinazzi, who had pulled to the side of the track with an apparent engine problem.
It was the second red flag of the session as not long after the commencement of Q1, Robert Kubica's Mercedes engine started billowing smoke before he could lay down a lap time.
Bahrain International Circuit - Winter testing