The 58-year-old Maradona took over in September and took the team that was near the bottom in the standings to consecutive final series in the Apertura 2018 and Clausura 2019 tournaments.
Both times, the team fell to Atletico San Luis, which reached the top flight.
"Diego Maradona decided to not continue as the head coach of Dorados," Maradona's manager, Matias Morla, said on his Twitter account. "On medical advice, he will dedicate time to his health and will have two surgeries: in the shoulder and knee. We are thankful with the Dorados family and will continue the dream together in the future."
In January, Maradona was admitted to a hospital in Argentina suffering from stomach bleeding, just a few days before returning to Mexico for his second season with Dorados.
Maradona's orthopaedic surgeon, German Ochoa, said earlier this year that the former soccer star has no cartilage left in his knees due to severe osteoarthritis and will need prostheses.
"Together we shocked the world. We showed that soccer is all about passion and heart, you will always be a Dorado, thanks for everything Diego," the club tweeted. "Get well and we'll see you soon."
Maradona is one of the most recognizable names in international soccer, having led Argentina to the 1986 World Cup championship in Mexico with his infamous "Hand of God" goal.
His arrival to Sinaloa, considered the heartland of drug-trafficking in Mexico raised eyebrows due to Maradona's troubles with addictions in the past. But in his nine month-stint in Mexico, he never got into trouble outside the pitch and led his team close to the first division.
"I was on the brink of dead, to me, this ... is nothing", said Maradona after losing the Clausura finals. "I'm just sad for the guys on the team."