Cranston won the prize for Best Actor in a Drama Series, while the show was declared Best Drama Series.
"This is such a wonderful honor and such a wonderful way to say goodbye to a show that has meant so much to me," Cranston told the crowd.
The actor played a cancer-stricken chemistry teacher-turned-methamphetamine kingpin for five seasons on the series, which wrapped up last fall.
Robin Wright earned the prize for Best Actress in a Drama Series for her work in the Netflix show "House of Cards."
Celebrity Families of 2014 [PHOTOS]