"This action is the most recent step in the Justice Department's effort to attack every aspect of the cartel's operations," US attorney general Merrick Garland said on Saturday.
Mexican security forces captured Guzman Lopez, alias "the Mouse", in January in Culiacan, the capital of Sinaloa state, the cartel's namesake.
Three years earlier, the government had tried to capture him but aborted the operation after his cartel allies set off a wave of violence in Culiacan.
January's arrest set off similar violence that killed 30 people in Culiacan, including 10 military personnel.
The army used Black Hawk helicopter gunships against the cartel's truck-mounted .50-calibre machine guns.
Cartel gunmen hit two military aircraft forcing them to land and sent gunmen to the city's airport where military and civilian aircraft were hit by gunfire.
On Friday, Garland recognised the law enforcement and military members who had given their lives in the US and Mexico.
"The Justice Department will continue to hold accountable those responsible for fuelling the opioid epidemic that has devastated too many communities across the country," he said.
Mike Vigil, former head of international operations for the Drug Enforcement Administration, said he believed the Mexican government facilitated the extradition because, for someone of Guzman Lopez's high profile, it usually takes at least two years to win extradition as lawyers make numerous filings as a delaying tactic.
"This happened quicker than normal," he said.
In April, US prosecutors unsealed indictments against Guzman and his brothers, known collectively as the "Chapitos".
They laid out in detail how following their father's extradition and eventual life sentence in the US, the brothers steered the cartel increasingly into synthetic drugs such as methamphetamine and the powerful synthetic opioid fentanyl.
The indictment unsealed in Manhattan said their goal was to produce huge quantities of fentanyl and sell it at the lowest price.
Fentanyl is so cheap to make that the cartel reaps immense profits even wholesaling the drug at 50 cents per pill, prosecutors said.
The brothers denied the allegations in a letter.
The Chapitos became known for grotesque violence that appeared to surpass any notions of restraint shown by earlier generations of cartel leaders.
Vigil described Guzman Lopez as a mid-level leader in the cartel and not even the leader of the brothers.
"It's a symbolic victory but it's not going to have any impact whatsoever on the Sinaloa cartel," he said.
