Modise replaces Baleka Mbete, who headed the House as Speaker for two terms since 2009.
Former Johannesburg Mayor Amos Masondo will become the new chairperson of the NCOP, according to the ruling party on Monday.
The ANC's has also indicated that of Environmental Affairs Minister Nomvula Mokonyane will be transferred from President Cyril Ramaphosa's cabinet to become the new National Assembly chairperson responsible for portfolio committees.
Despite the move being appearing to be a demotion, chairing the national assembly is still a powerful position in parliament as the "chair of chairs" oversees the work of the National Assembly's committees, approves trips and also presides over plenary sessions of the assembly.
With the filling in of the senior posts in both Houses, members of parliament should be sworn-in this week ahead of a nomination for the president and his swearing-in on 25 May.
Incumbent President Cyril Ramaphosa is expected to reprise his role as head of state due to the majority command his party has in parliament.