In Saturday's penultimate round, four of six remaining candidates withdrew: Sally Boynton Brown, Samuel Ronan, Jehmu Greene and Peter Peckarsky.
Perez, 55, had narrowly missed winning in that first round by a single vote. He had courted the party establishment, while Ellison, 53, was backed by the party's progressive left.
Succeeds Donna Brazile
Perez succeeds outgoing interim chairwoman Donna Brazile, who stepped in last year after internal communications stolen by hackers were leaked.
Both final candidates had promised major efforts to rebuild party infrastructure at the local and state level, which withered across the US despite former president Barack Obama's personal ratings.
Perez said the Democrats had lost about 1,000 electoral posts from Capitol Hill to state legislatures over the past decade - in addition to Hillary Clinton's presidential defeat in November.
The party had been facing a "crisis of confidence," he told 427 eligible party delegates Saturday.
Ellison said the party must prioritize small donations and switch from anti-Trump "demonstration energy to electoral energy."
Perez backed by Obama
Perez entered the chairmanship race urged by former President Barack Obama. Ellison had endorsements from Senate Minority Leader Chuck Schumer and Vermont Senator Bernie Sanders, who last year challenged Clinton for the Democratic nomination.
Cybersecurity experts had worked with the party to address vulnerabilities, Brazile told the DNC committee.
She chided President Trump for his mockery of Democrats for cybersecurity lapses, saying: "No, Donald Trump, you can't go to Staples [business equipment store] and buy anti-Russian hacking software."
Republican party officials insist that their party communications were not breached.