Ramaphosa announced a total of 30 changes to minister and deputy minister positions after Zuma was forced to resign by the ruling ANC party earlier this month.
"In making these changes, I have been conscious of the need to balance continuity and stability with the need for renewal, economic recovery and accelerated transformation," Ramaphosa said, reading a brief televised statement.
Nene's return to the finance ministry was a clear repudiation of Zuma's reign.
In December 2015 Zuma sacked the widely respected Nene and replaced him with a little-known MP, triggering panic among investors and a sharp drop in the rand currency.
Although several Zuma allies were demoted or sacked, Zuma's ex-wife Nkosazana Dlamini-Zuma was appointed minister to the presidency, responsible for planning, monitoring and evaluation.
Ramaphosa narrowly beat Dlamini-Zuma in a fierce contest to be elected the new leader of the ANC in December.
David Mabuza, the current premier of Mpumalanga province, was named deputy president.
Mabuza's appointment is likely to stir controversy due to his reputation as a tough hardliner and accusations of links to political violence.
The opposition Democratic Alliance (DA) party said Ramaphosa choosing Mabuza "undermines the integrity of his stated commitment to fight corruption and rebuild from the tatters of the Zuma decade".
Mabuza "has been accused of having his own personal 'military' which have allegedly been responsible for numerous political killings", the DA added.