The Supreme Court said a lower court in southern Karnataka state had wrongly summoned Dhoni over the case, one of several brought mainly by Hindu nationalists accusing him of hurting religious sentiments.
"(We) quash the proceedings including the summoning order against the accused... we have taken note of the complaint and the offence alleged while passing this order," a bench headed by Justice Ranjan Gogoi said, according to the Press Trust of India.
The controversy dates back to 2013 when Business Today magazine ran a drawing portraying Dhoni as Hindu god Vishnu, holding various products representing his wide-ranging endorsement deals, including a shoe.
Hindu nationalists lodged criminal complaints to police against him in different parts of the religiously diverse but Hindu-majority country, although most were later dismissed.
The Supreme Court stayed criminal proceedings against Dhoni last year after he appealed against the case in the Karnataka High Court lodged by an activist -- before the top court quashed the proceedings on Monday.
The top court also stayed in January an arrest warrant issued for Dhoni by a lower court in southern Andhra Pradesh state for failing to answer repeated summons to appear there over the same issue.