Other alleged plotters are still being hunted over the powerful bomb found planted in a trash can near the US embassy in Manila on Monday, said the capital's head of police, Chief Superintendent Oscar Albayalde.
"They were detained as persons of interest in the planting of the IED (improvised explosive device)," he told AFP of the arrested pair.
"There is a real possibility that this is the handiwork of the Maute group," he said, referring to an armed Muslim extremist group that has previously pledged allegiance to the Islamic State movement in Syria and Iraq.
Albayalde added they were hunting for "three to five other suspects," but declined to give details.
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The Maute group has also been blamed for a bomb that injured seven military bodyguards of President Rodrigo Duterte and two other soldiers in Mindanao on Tuesday.
The group recently occupied part of the remote mountain town of Butig in the troubled southern Philippines island of Mindanao, prompting the military to launch an offensive.
Duterte visited Butig town 800 kilometres (500 miles) south of Manila on Wednesday, conferring with military officers and local officials and later meeting with wounded soldiers.
Military spokesman Major Filemon Tan said most of Butig had been recaptured from the Maute group with 61 of the extremists slain and 12 wounded, compared to 35 injured on the government side.
But the Maute group has weathered military assaults before, having been driven from Butig in a previous offensive in February.
"I do not want to wage war but do not force my hand to do it," he said.
Muslim groups have waged a decades-long armed independence struggle in the south of the mainly Catholic Philippines that is believed to have claimed more than 120,000 lives.
On Monday, Duterte said IS, which controlled vast swathes of Iraq and Syria, had linked up with the Maute gang, a departure from previous military denials of formal links between IS and local extremist groups.