Two-time MotoGP champion Francesco Bagnaia, who had come into the weekend in Alcaniz with a five-point lead in the world championship over Martin, dropped several places to finish a lowly ninth after qualifying third on the grid.
Martin now leads Bagnaia by three points and will have the opportunity to extend that lead in Sunday's race.
"It was a fantastic race after the crash in qualifying made it difficult to gain the confidence, but finally I tried to follow Marc," Martin said.
"I thought maybe at the end I could do something but it was impossible, so congrats to him but I feel confident that tomorrow I can make a step and find him."
It was Marquez's first sprint win with Ducati, having switched from Honda ahead of this season.
"My start was a little bit stiff but then I started to ride in a better way," Marquez said.
"The most important day is tomorrow, so today we celebrate because this feels great, but it's really important for us to win the sprint race.
"I'm looking forward to tomorrow, racing in front of these amazing people."
Fellow Spaniard and Red Bull GasGas Tech3's 20-year-old rookie Pedro Acosta put on an impressive display to complete the podium.
Marquez's brother and teammate Alex made up one place to finish fourth.
Enea Bastianini, who had a frustrating morning after the Italian Ducati rider finished fourth in the first qualifying session, made up several positions to come seventh.
