The incumbent, who is seeking a second and final term in office, has the support of 56.5 per cent of the 1,102 respondents polled by Roy Morgan, a Melbourne-based market research firm, last month.
The result was 0.5 percentage point lower than what Mr Joko scored in a previous survey in February, while support for Mr Prabowo rose by the same margin to 43.5 per cent.
A further breakdown of the results shows that Mr Joko, better known by his moniker Jokowi, is the choice of more than six in 10 rural voters surveyed.
Among urban voters, however, the difference between the two candidates was far narrower, with the President ahead of his opponent 51.5 per cent to 48.5 per cent.
“Despite trailing Prabowo, support for Jokowi in Jakarta, West Java and Banten has increased in March from a month ago,” said the Roy Morgan researchers.
Mr Prabowo, however, has also gained an advantage on the islands of Sulawesi and Kalimantan, they added.
While the latest results show that Mr Joko and his running mate Ma’ruf Amin are still on course for an election victory, it also confirms a survey by Kompas newspaper last month that showed Mr Prabowo and vice-presidential hopeful Sandiaga Uno gaining momentum as polling day looms.
The pre-election poll by Kompas, released on March 20, had shown support for the President falling below the 50 per cent psychological mark for the first time, and his rivals gaining significant ground.
Indonesia’s largest newspaper said its findings indicated that the electability of Mr Joko and Dr Ma’ruf dropped to 49.2 per cent from 52.6 per cent six months ago.
In contrast, support for Mr Prabowo and Mr Sandiaga rose to 37.4 per cent, up almost five points from the previous survey by Kompas released in October last year.
The Roy Morgan results may go some way to vindicate the findings of the Kompas survey, which were viewed by some with scepticism when released last month.
This was because its findings seemed to go against the grain of most, if not all, other surveys, including many showing Mr Joko with a double-digit lead.
The Prabowo-Sandiaga ticket has made inroads when seen against another Roy Morgan survey in December when they scored 40.5 per cent, behind the Joko-Ma’ruf ticket’s 59.5 per cent.
This means the challengers have gained three percentage points in the Roy Morgan survey from December last year, while support for the incumbent and his vice-presidential pick has fallen by the same margin.
But even as Mr Prabowo closes in on the incumbent, Ms Levine believes the presidential race is still really Mr Joko’s to lose.
“Although support for Prabowo has now increased for two straight months, time is running out for the challenger to close the gap on the President,” said Ms Levine.