"I would like to congratulate President Trump. Long live!" Duterte said to applause on Wednesday. "Now we're here, I don't want to ... fight because Trump is already there."
The traditional alliance between the United States and the Philippines had been strained since Duterte called Obama a "son of a bitch
" in September.
One month later, during a visit to China in October, Duterte said the US alliance was over, claiming "America has lost."
But one day after Trump won the 2016 United States presidential election, the Philippines president said he and Trump had a shared trait, and that some military exercises would be back on.
"We both like to swear. One little thing, we curse right away, we're the same," Duterte said of Trump on Wednesday.
Philippines agrees to limited US exercises
At the lowest point of US-Philippines relations in early October, Duterte announced there would be no more military drills between the two countries for the foreseeable future.
He later amended that to say in the "next year."
But in a statement on Thursday, Philippines National Defense Secretary Delfin N. Lorenzana said Duterte had agreed to continue military training with the United States.
Lorenzana confirmed assault exercises and some bilateral drills would be off the table, with a focus instead on joint training and exercises.
Sydney's Lowy Institute International Security Program Director Euan Graham said Duterte wanted to focus on building up internal security while avoiding antagonizing China with drills in the South China Sea.
"As far as possible he wants to get out of all fighting with the US so that he minimizes the collateral cost to the China relationship. That's the game he's playing," Graham said.
"I think that it's more advanced that either kowtowing to Beijing or the United States."
Graham said while the United States alliance with the Philippines was safe for now, Duterte might discover it was harder to play the two superpowers off against each other than he thought.
"Ultimately it depends on how willing the US and China are to put up with his antics and I think this is the still the honeymoon period for (Duterte)," he said.
Controversial Philippines leader
Philippines President Duterte has attracted a huge amount of controversy since he took office in late June.
Hundreds of alleged drug dealers and users have died since came into power as part of his countrywide war on drugs, including officials such as a local mayor who was shot dead
Duterte has also made numerous controversial comments against his rivals and other foreign leaders, including Obama who he told to "go to hell"
earlier in 2016.
A meeting will be held between the US and Philippines military officials on November 22 to begin planning for next year's drills.