They were told to put their right hands over their left, but two ASEAN world leaders were still confused with the ceremonial handshake.
Mr Duterte, who has spoken highly of Mr Trump, said last week he would tell the United States president to "lay off" if he were to raise accusations of rights violations.
"Give us your brightest smile", an emcee intoned, as the leaders lined up onstage for their star turn.
The Indian Prime Minister arrived in the Philippines capital on Sunday for a three-day visit.
But Trump could not quite do that, nor could he muster the ritual greeting. The two men also shared a laugh in the meeting when Duterte called reporters "spies", the Associated Press reports.
The issue was discussed during the Modi-Trump meeting yesterday and is understood to have figured in the Prime Minister's talks today with both Abe and Turnbull.
"President Trump expressed his condolences for the tragic loss of life in Marawi City at the hands of ISIS-affiliated terrorists, and congratulated the Armed Forces of the Philippines for its success in liberating Marawi", according to a joint statement released after the bilateral meeting between Trump and Philippine President Rodrigo Duterte on Monday, November 13.
Handshakes have long held outsized significance for Trump, who uses the phalangeal greeting to size up potential rivals, assert his dominance, or convey warm sentiments.
Donald Trump's handshake is now well-known as one of the USA president's signature power plays, but in the Philippines he was left perplexed when forced to use both hands during the pageantry of a photocall.
And a March photo opportunity, in which Trump failed to shake hands with German Chancellor Angela Merkel in front of cameras, was viewed as a snub of the German leader.
"I get along very well with Angela", he said.