Villalobos will replace retiring Principal Noreen Likins at Gunn, and Winston will replace departing Principal Jacqueline McEvoy at Paly.
Both nominees have worked most recently at Gunn, where Villalobos currently teaches history and Winston is an assistant principal.
The two will be presented to the Board of Education for confirmation May 11.
"I am extremely pleased to have two great recommendations to bring to the board, both of whom come from our own talented administrative staff," Superintendent Kevin Skelly said in a statement Thursday.
"Ms. Villalobos and Mr. Winston carry institutional history that is invaluable to the district as the organization moves ahead."
Villalobos, who was born in El Salvador and moved to San Francisco when she was 4, began her teaching career at Paly in 1996. She became the assistant principal at Paly in 2002 and served as principal at Capuchino High School in the San Mateo Union High School District for one year before returning to Palo Alto in 2008.
She received her bachelor's degree in political science from UCLA and her masters in public administration from Notre Dame de Namur University.
"After all the administrative work I just wanted to get back in the classroom," Villalobos said upon returning to Palo Alto two years ago. "I love being around students."
Villalobos said she wanted to teach history for as long as she can remember.
"I have a fascination with old stuff," she said in a two-year-old school publication, "New Faces at Gunn.
"I'd say my dad was my first history teacher. We were always playing games and having conversations relating to history. History is part of me — it's who I am."
Winston began his teaching career in the Milpitas Unified School District where he taught for six years. In 2005 he joined the Palo Alto district as a teacher at JLS Middle School. In 2006 he was named dean of students at Gunn, becoming an assistant principal in 2007.
Winston received his bachelor's degree in psychology from California State University, Hayward, and a master's in special education and a master's in educational administration from Santa Clara University.
Winston's duties at Gunn have included developing and monitoring the school budget, coordinating campus supervisors, discipline, field trips, special testing arrangements, supervising substitute teachers, monitoring attendance and tracking textbooks.
Thursday's announcement takes Skelly a step further in replacing top leadership that have announced departures from the financially stressed school district.
The school board earlier this week confirmed the appointments of Anne Brown and Katherine Baker, who replace retiring principals Lupe Garcia of Palo Verde Elementary School and Carmen Giedt of Terman Middle School, respectively.
Also departing in June are Assistant Superintendent Linda Common, Director of Student Services Carol Zepecki, Secondary Education Director Burton Cohen, Curriculum Services Coordinator Barbara Lancon and Paly Assistant Principal Todd Feinberg.