He took 53 per cent in 2014, winning 8.4 million more votes than the former general, Mr Prabowo, who also ran at the last election.
This suggests the incumbent has little to gain from such a fraud, which accounts for less than half a percent of eligible voters.
Since the video was released, both sides have claimed the other was responsible. The Prabowo camp was quick to jump on the incident.
“The emergence of the video which shows ballots cast for the candidates on the number 01 ticket [President Jokowi] … clearly indicates that electoral fraud exists,” an opposition spokesman said in a statement.
The President said a team had been sent to Malaysia to investigate, while one of his coalition partners said the incident was part of a “dirty tricks” campaign orchestrated by an opposition scared of losing.
Indonesia’s former Foreign Minister, Marty Natalegawa, worried such incidents would leave people disillusioned with “our democracy”.
“Issues are no longer resolved, they are simple overtaken by new issues,” he said during an interview on Friday.
“Overall the trajectory of our democracy is very positive, but we need to ensure we are not backsliding, we can’t be complacent.”
Wednesday’s poll, where 192 million people are eligible to vote, is the sixth free election since the fall of President Soeharto in 1998.
The video purports to show 20 diplomatic bags, 10 garbage bags and five rice sacks filled with ballot papers marked for Mr Widodo.
The Prabowo camp claimed earlier this month there were 17.5 million ghost voters on the electoral role.
At a press conference, Mr Prabowo’s brother, the billionaire businessman Hashim Djokohadikusumo, said this raised questions around the legitimacy of the election result.
“There is a clear possibility we will go to the Constitutional Court and yes, Prabowo-Sandi supporters may not accept the result,” he said referencing his brother’s running mate Sandiaga Uno.
Analysts believe the President needs to win more than 55 per cent of the vote to blunt claims of fraud, which could see people take to the streets and plunge Indonesia into months of uncertainty while the Constitutional Court makes its ruling.