It was contested by Qonde of Gweb, which received 148 votes to Nzimande’s 266 votes.
Employment and Labor minister Thulas Nxesi will be the deputy chair for SACP.
Nzimande’s return to the helm was not without drama, however, as some members who opposed him struggled to find a formidable opponent to challenge him.
Several names were thrown into the fray, although some fell short of the appointment threshold.
Solly Mapaila, who for years served as Deputy General Secretary, was unanimously elected as General Secretary.
Madala Masuku is now the first deputy secretary general, while deputy treasury secretary David Masondo is the new second deputy secretary general.
Meanwhile, Joyce Moloi-Moropa returns as National Treasurer.
The congress, which took place in Boksburg and was attended by African National Congress president Cyril Ramaphosa, ends on Saturday.
Ramaphosa addressed the SACP Congress on Friday touching on the Phala Phala farm robbery scandal threatening to end his reign in South African politics.
The underfire president said he will not be intimidated by his critics but however assured delegates that he was not above the law and would respect the findings of the investigation.