Pramac rider Martin is 26 points in front of pole-sitter Bagnaia ahead of the main event Grand Prix on Sunday after charging to an unexpected second sprint win 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 Ducati's Bagnaia for the rest of the 13-lap sprint and crossed the finish line 1.495 seconds in front of his Italian rival, improving his position at the top of the standings.
"Today I expected maybe to be fighting with Pecco (Bagnaia) but I didn't expect to do that start," said Martin.
"I even had a gap to keep for the last two laps so super happy. For tomorrow it's another story but I feel confident that we are in a good way, super good and super fast."
Martin has not won a GP since the French back in May but his consistency has helped him accumulate a decent advantage as he searches for his first MotoGP title.
The 27-year-old had finished second in both the sprint and GP at four of the previous 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.
'Disaster start'
It was a big blow for Bagnaia, who was favourite to cut the gap separating him from Martin after claiming pole position with a record-breaking fastest lap at the "Marco Simoncelli" circuit earlier on Saturday.
Two-time champion Bagnaia is riding with injuries to his shoulder, neck and collarbone after crashing out of last weekend's Aragon MotoGP but looked in great form before Martin left him for dust.
"I'm absolutely not happy... The start was a disaster, I lost first position and from that moment it was very difficult," said Bagnaia.
"In any case, second position after what happened last week is OK. We will work to improve the start because it was a disaster and try to be in a better shape tomorrow."
Bagnaia is at least helped by this weekend being the first of two in a row at the Misano, as the same circuit is being used later in September for the Emilia Romagna GP which replaces the cancelled race in Kazakhstan.
Marc Marquez, a double winner at Alcaniz last weekend, had a harder time in Italy and lost ground on Martin, dropping to 77 points off the summit in third after finishing the sprint in sixth place.
Six-time champion Marquez battled up the rankings from his starting position of ninth on the grid, but has been caught on 234 points by Enea Bastianini.
