The choice of Budi Gunawan, suspected by the Corruption Eradication Commission (KPK) of receiving bribes, casts doubt on Widodo's campaign promise to deliver clean governance in Southeast Asia's biggest economy, where endemic corruption can be a dampener on investment.
Parliament, which has a patchy record on graft, endorsed Gunawan on Thursday with a near unanimous vote, clearing the way for his inauguration as police chief.
"People had very high expectations of Jokowi to stand up to corruption and they will be very disappointed if he goes ahead (with the choice)," said one of the President's supporters, Agus Sunaryanto, who is an official of Indonesia Corruption Watch.
He was referring to the President by a popular nickname.
Indonesia is at a crossroads, the Jakarta Globe, an English-language daily, said in an editorial.
"If (Gunawan) is inaugurated, Indonesia will have a graft suspect as police chief, a humiliation for the nation, and Widodo will face nationwide protest from the very people who helped him become president," the Globe said.
Gunawan is close to Megawati Sukarnoputri, former President and leader of Widodo's political party, and many consider the nomination a political manoeuvre aimed at appeasing Megawati.
Mr Widodo has said he chose Gunawan on a recommendation from the National Police Commission.
Mr Widodo, a former furniture businessman who is seen as a break with Indonesia's entrenched political establishment, narrowly won last year's presidential race and took office in October.
But Indonesians this week took to social media to criticise him, with hashtags such as "ShameOnYouJokowi" and "WhereAreYouMrPresident" trending on social media website Twitter.
The KPK, a hugely popular agency with a perfect record of convictions, has been investigating suspect bank accounts held by Gunawan since last July.
This week it imposed a six-month travel ban on Gunawan and expects to start questioning witnesses "soon", a KPK official, who asked not to be named because he was not authorised to speak to the media, told Reuters.
Gunawan on Thursday told a parliamentary hearing to consider his nomination that he had never been interrogated by the KPK over the case, local media reported.
But anti-corruption activists still held out hope for Mr Widodo to withdraw his choice of police chief.
"I hope Jokowi will surprise us," said Sunaryanto.