Butkovitz clinched the primary win with a 2-1 margin, taking 61 percent of the vote to Mandel's 31 percent with 95 percent of the votes counted.
Mark Zecca, a 20-year veteran of the city's Law Department, trailed with 8 percent.
Butkovitz credited his office's audits of the Sheriff's Office and charter schools with establishing himself as an independent fiscal watchdog for city tax dollars.
The low voter turnout made this a party-driven election, and Butkovitz said his Democratic Party endorsement was a factor.
"I think the fact that I've had a long record, mostly with the public but also with leaders in government and the community, sure, that helped," Butkovitz said.
Mandel, who built a stronger campaign infrastructure and had more resources than four years ago, said the light voter turnout was a disappointment.
"You'd like to think more people would be involved," Mandel said. "We did all we could to reach out to people, to engage them one-one-one."
The primary was particularly nasty for Butkovitz and Mandel, a tax-policy advocate who served as a top aide to former City Controller Jonathan Saidel.
Butkovitz, a long critic of the Actual Value Initiative, which will change the way the city taxes property, attacked Mandel for going to court in a failed bid to spur the program's implementation.
Mandel derided Butkovitz as a cog in the city's political machine who didn't perform the basic functions of his office while seeking another term as a platform to run for mayor.
Both men confirmed meeting last year to discuss ways to avoid a primary contest. One option pitched was for Butkovitz to hire Mandel. No deal was struck.
Zecca, poorly funded and little-known, gamely tried to offer himself as alternative.
Butkovitz, a ward leader who served as state representative for a Northeast Philly district from 1991 until his election as controller in 2005, has been coy about his future political ambitions.
"You don't run for mayor," Butkovitz claimed in an April 15 debate. "It just happens to you."
On Twitter: @ChrisBrennanDN