Munster lead the way with six players as Jaco Taute, Rory Scannell, Tyler Bleyendaal, Dave Kilcoyne, John Ryan and Billy Holland all included.
The pack includes Leinster pair Dan Leavy and Jack Conan plus Scarlets duo Ken Owens and James Davies.
Connacht's Tiernan O'Halloran, Glasgow wing Tommy Seymour and Edinburgh's Ben Toolis also make the Dream Team.
Pienaar earns recognition as he prepares to leave Ulster following seven years at the Irish province.
The IRFU refused Ulster's request to extend the South African's contract and the scrum-half is set to join Montpellier.
Journalists and broadcasters from across Ireland, Scotland, Wales and Italy chose the Pro12 Dream Team.
The Pro12's awards night takes place in Dublin on Sunday.
2016-17 Guinness Pro12 Dream Team
T O'Halloran (Connacht); T Seymour (Glasgow Warriors), J Taute (Munster), R Scannell (Munster), C Piutau (Ulster); T Bleyendaal (Munster), R Pienaar (Ulster); D Kilcoyne (Munster), K Owens (Scarlets), J Ryan (Munster); B Toolis (Edinburgh), B Holland (Munster); D Leavy (Leinster), J Davies (Scarlets), J Conan (Leinster)
Ulster's Ruan Pienaar and Charles Piutau have been named in the Pro12's team of the season.