A joint session of the House of Representatives and the Senate in Manila endorsed the official count of this month's election, which saw the trash-talking politician who revels in threats to kill criminals win by more than six million votes.
Duterte declined to attend the nationally televised event, preferring to remain more than 900 kilometres away in his southern hometown of Davao that he has ruled as mayor for most of the past two decades and he admits is his comfort zone.
Duterte, 71, won the elections largely due to an incendiary law-and-order platform headlined by a vow to wipe out crime within six months.
He pledged to give security forces shoot-to-kill orders, and vowed that tens of thousands of criminals would die. Since the election Duterte has continued to encourage police to kill drug suspects, and said he would bring back the death penalty.
More From This Section
Another key message of Duterte's campaign was his pledge to take on the nation's political and economic elite, selling himself as an explosive political outsider that could shake up a power structure overseeing one of Asia's biggest rich-poor divides.
Since the elections, Duterte has refused to travel to Manila and promised to remain in Davao until he assumes the presidency.
This has forced politicians, powerbrokers, business leaders and courtiers to fly to Davao for an audience.
In further blows for so-called "Imperial Manila", Duterte has named many politicians from the southern Philippines to cabinet posts.
Duterte has also repeatedly expressed his disdain for spending time in Manila, describing it last week as a "dead city" overrun by slums.
Duterte's absence at the Manila ceremony today delivered a message that he would not be beholden to lawmakers, said Ramon Casiple, executive director of the Institute of Political and Economic Reforms.
"As a symbolism he simply doesn't want to be confined by Congress," Casiple told AFP.
However even some of Duterte's supporters were disappointed that Duterte shunned such an important date on the Philippines' democratic calendar.