The series about schoolteacher Walter White, who begins making and selling methamphetamines to care for his family after a terminal cancer diagnosis, concluded last year after five seasons.
"Holy cow!" exclaimed "Breaking Bad" creator Vince Gilligan when accepting the Emmy statuette, U.S. television's highest honor.
"This is indeed a wonderful time to be working in television ... we're all lucky to be working now," added Gilligan, whose show picked up five Emmys for cable network AMC.
"Breaking Bad" held off upstart "True Detective," Netflix's online political thriller "House of Cards," HBO medieval fantasy "Game of Thrones," PBS British period series "Downton Abbey" and AMC ad world portrait "Mad Men."
The annual Emmys, which are handed out by the Academy of Television Arts and Sciences, pitted cable and online newcomers against traditional cable and network heavyweights, with the Academy picking old favorites over cable and Internet upstarts.
In comedy, ABC's "Modern Family" about unconventional families won best series for the fifth consecutive year, tying 1990s NBC sitcom "Frasier" for the most comedy victories.
"'Modern Family' has been a big, beautiful dream for the last five years and we thank you for not waking us up," said series co-creator Steven Levitan.
"Breaking Bad" streaked through its final Emmys as Bryan Cranston, who portrays Walter White, won for best actor in a drama while co-stars Aaron Paul and Anna Gunn each won for their supporting roles.
Juliana Margulies won best drama actress for her role as lawyer Alicia Florrick in CBS's "The Good Wife."
SOMBER WILLIAMS TRIBUTE
Although the big broadcasters were shut out of the nominations for best drama and have taken a backseat to cable and Netflix in recent years, they notched several early wins among comedies, with CBS picking up a leading five wins alongside AMC and FX.
HBO earned four wins, while broadcasters ABC and PBS each earned three. Netflix, which earned nominations for political thriller "House of Cards" and comedy "Orange Is the New Black" was shut out in top awards.
Jim Parsons won his fourth lead acting Emmy for playing the pedantic nerd Sheldon in the CBS comedy "The Big Bang Theory," and Julia Louis-Dreyfus won her third consecutive Emmy for her role as the foul-mouthed, gaffe-prone U.S. Vice President Selina Meyer on HBO's political satire "Veep".
"Fargo" gave FX Networks its first Emmy for a program, but actors from the critically acclaimed miniseries lost out on awards despite being heavy favorites, especially lead actor Billy Bob Thornton.
The Emmys, which were hosted by comedian Seth Meyers in Los Angeles, were moved up from their usual Sunday night spot in September so as not to conflict with NBC's ratings-powerhouse "Sunday Night Football" and MTV's Video Music Awards.
The celebratory program assumed a somber tone when actor Billy Crystal paid a cosmic tribute to friend and comedian Robin Williams, who died in an apparent suicide two weeks ago.
In the comedy awards, comedian Louis C.K. won his second writing award for his FX show "Louie," and Stephen Colbert's Comedy Central fake news show "The Colbert Report" won the Emmy for best variety program for the second consecutive year.
British television miniseries "Sherlock: His Last Vow" won three Emmys for U.S. public broadcaster PBS.
HBO's "The Normal Heart" earned best TV movie honors for its depiction of the early fight against AIDS.
