The DA complained to the police watchdog following video posted by TimesLIVE last week showing the league's president, Julius Malema, ordering police officers to eject rival delegates from the conference.
Malema has been accused by his rivals in Limpopo of having ''stolen" the conference with the help of the police.
His preferred candidate won the election.
Supporters of an opposing group, led by Lehlogonolo Masoga, were chased out of the hall. The conference ended in chaos.
Malema's opponents allege that the police helped remove the rival delegates after being told to do so by the ANCYL president.
TimesLIVE has exclusive video from inside the venue which you can watch in related video on the right
But police in Limpopo this week denied the accusations, saying they did not get instructions from Malema, and that they acted after the situation at the conference had ''got out of hand".
Limpopo police spokesman Col Motlasela Mojapelo could not be reached for comment on the Independent Complaints Directorate's decision to investigate.
DA MP Dianne Kohler Barnard welcomed the decision, saying ''the impartiality and integrity of the police must be maintained at all costs".
Kohler Barnard said: ''We cannot permit a situation in which police officers follow orders given to them by civilians, and for party-political reasons.
''The South African Police Service Act clearly stipulates that no [police officer] may further or prejudice party-political interests, and that no [police officer] shall publicly display or express support for, or associate himself with, a political party, organisation, movement or body."
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