Trump told reporters outside his Florida home that he and Obama had a "very nice" and "general" conversation.
The phone call came after an abstention vote on an Israel-related resolution from the US prompted Trump to question the decision on Twitter.
"We cannot continue to let Israel be treated with such total disdain and disrespect. They used to have a great friend in the US, but..." read a Trump tweet early Wednesday.
Trump also tweeted that the transition process was not smooth. He pledged to do his best to "disregard the many inflammatory President O statements and roadblocks. Though it was going to be a smooth transition-Not!"
The harsh words may have been connected to an earlier remark from Obama that he could have beaten Trump if they went against each other in an election.
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