Metropolitan Police Constable Alex MacFarlane was recorded allegedly making the comments to a suspect arrested days after the riots last summer.
The decision follows a review of the evidence after the CPS decided not to press charges earlier this year.
Alison Saunders, chief prosecutor for London, said the original decision had been "regrettable, but added that a prosecution was necessary to maintain public confidence.
Ms Saunders said: "As Chief Crown Prosecutor for London, I have taken the decision in this case that, as well as there being sufficient evidence for a realistic prospect of conviction, and a prosecution being in the public interest, a prosecution is necessary in order to maintain confidence in the criminal justice system."
Another allegation of abuse by a police officer against a youth at Forest Gate police station remains under consideration, the CPS said.
The decision to charge Mr MacFarlane came as Metropolitan Police Commissioner Bernard Hogan-Howe gave evidence to the Home Affairs Select Committee about ongoing claims of racism within the force.
He stressed that the claims against Mr MacFarlane were only allegations but said he was pleased that prosecutors had reviewed their original decision.
He told MPs: "We have to let the criminal case take its course. I'm glad that it will be tested in court."
Mr Hogan-Howe said the Met would now take a decision on misconduct proceedings in the officer.
He also reaffirmed his determination to stamp out racism and tackle the suggestion that the force has not learnt the lessons of the Macpherson report, which concluded that the Met was "institutionally racist".
He told the committee: "I condemn any racist in the Met. I am not going to stand for them being in the Met, and I will drive them out. Whatever is in my power to do something about that, I will do,"
Asked by MPs about security preparations for the Olympics and the Queen's Diamond Jubilee, Mr Hogan-Howe admitted he could not guarantee there would be no repeat of the sort of protest that disrupted the University boat race.
He said security arrangements were under constant review but there were limits what you could do with events held in large open spaces.
"I have to sit here and tell you I can't guarantee that when we have large events in public spaces we can guarantee that there will not be an embarrassment about some level of protest. Our main issue is to make sure people are kept safe," he explained.