The 72-year-old defence minister declared before jubilant supporters late on Wednesday that it was a "victory for all Indonesians."
Quick ballot counts by independent pollsters showed he won nearly 60% of votes, surpassing pre-election projections of a slim majority. Such counts have proven accurate in past votes.
The veteran politician with a hardline military past had an insurmountable lead over rivals, ex-governors Anies Baswedan and Ganjar Pranowo, who trailed at least 33 points behind.
The national election agency is expected to announce official results by March 20.
"His apparent one-round victory should remove uncertainty over who will lead the next administration," said Barclays economist Brian Tan. "He appears to be the outgoing President Joko Widodo's choice of successor and has promised policy continuity, which should provide some reassurance to investors."
Jokowi, as the popular incumbent is known, did not explicitly endorse any candidate, but Prabowo's running mate is the president's eldest son Gibran Rakabuming Raka, who is set to be the youngest vice-president in Indonesia's history.
The pair have pledged to continue Jokowi's efforts to position the resource-rich G20 economy as an electric-vehicle hub, extend a massive infrastructure and social assistance push, and create millions of jobs.
Second-place rival Anies, ex-governor of Jakarta who got 25% of the vote, said his team would wait for the official results and respect the people's decision.
Both Anies' and Ganjar's teams earlier said they were probing allegations of "systematic and massive fraud", but did not provide evidence.
Analysts have said there were no signs of electoral fraud.
But the days leading up to the vote were marred by protests against Jokowi, criticised over political interference after he made highly publicised appearances with Prabowo, and after a last-minute court ruling tweaked eligibility criteria, enabling his son to join the leading ticket.
Jokowi's allies have denied he meddled.
The world's biggest single-day election saw nearly 259,000 candidates vie for 20,600 posts across the archipelago.
In the legislative contest, parties backing Prabowo had about 42% of votes, while an alliance behind Anies had 27%, suggesting a Prabowo government could have strong parliamentary backing.
If confirmed, the new president will take office in October.
