Pramac rider Martin is 26 points in front of pole-sitter Bagnaia ahead of the main event Grand Prix on Sunday, after winning his second sprint of the season.
The Spaniard, who won at Misano Adriatico last year, started in fourth on the grid but got away like lightning and was ahead of Bagnaia by the first turn.
He comfortably held off Bagnaia for the rest of the 13-lap sprint and consolidated his position at the top of the standings.
Martin has not won a GP since the French back in May but his consistency has helped him accumulate a healthy advantage as he searches for his first MotoGP title.
He had finished second in the sprint and GP at four of the last five events and his display on Saturday means he cannot be overtaken in the standings this weekend by Bagnaia, regardless of what happens in Sunday's race.