Duterte is notorious for tangling with media outlets critical of his policies, sparking concern that press freedoms have been eroded in the Philippines.
"It's painful for us that we are being shut down, but it's also painful for millions of our countrymen who believe that our service is important to them," chairman Mark Lopez told viewers just before the main channel went dark.
Outside the company's broadcast compound, a handful of supporters waved placards against a backdrop of burning candles.
ABS-CBN's 25-year licence expired on Monday, but officials had previously given assurances the radio, TV and internet giant would be allowed to operate provisionally.
However, the National Telecommunications Commission's cease-and-desist order on Tuesday cited the expiration and said the outfit's operators would have to appeal for a return to the airwaves.
Early in his term, Duterte accused the network of failing to broadcast his 2016 campaign advertisements and not returning the payments made for them.0
Pressure groups said the shutdown order was an assault on the right to free speech, as the conglomerate broadcasts news coverage watched by millions daily.
The shutdown also comes as the nation battles to contain the coronavirus pandemic and an accompanying flood of online disinformation.