The pair connected after growing questions about a delay in the call between the uneasy allies.
"President Donald J. Trump spoke today with Chancellor Angela Merkel of Germany to congratulate her on her election victory and wish her well in the formation of her fourth government," said a statement from the White House on Thursday evening.
The US leader underscored the countries' "deep ties" and Washington's "commitment to our longstanding, strong alliance."
The White House did not immediately congratulate Merkel on her election over the weekend, as is customary, after a campaign which saw Merkel implicitly criticize Trump.
"It's obviously been a complicated relationship," said Karen Donfried, president of The German Marshall Fund of the United States.
That is unlikely to change in Merkel's fourth term.
"For her, clearly this is a critical relationship," she told AFP. "Merkel is still going to try to make the relationship work to the greatest extent possible."
"On Trump's side, my expectation is that he will stay very focused on his two big criticisms, one that Germany doesn't spend enough on defense and two that Germany has a 'massive trade surplus.'"
According to the White House, Trump and Merkel discussed the Iran nuclear deal and "how to counter Iran's malign activities in the Middle East," as well as the denuclearization of the Korean Peninsula.
Concerning the Iran deal Merkel has "renewed her support for this agreement, which is an important instrument to prevent Iran from equipping itself with nuclear weapons," according to a statement released by German government spokesman Steffen Seibert.