U.S. President Donald Trump wants a 20-percent border tax on all imports from Mexico, said White House spokesman Sean Spicer on Thursday.
It wasn't immediately clear what the pair talked about - or how cordially they greeted one another - but the call follows growing tensions between the North American neighbors.
USA president Donald Trump became embroiled in his first diplomatic spat on just his sixth full day in office after Mexico's president cancelled a meeting with him over his plans to build a border wall between the two countries.
Mr Pena Nieto condemned Mr Trump's order.
Trump insists that Mexico pay for the wall, while Pena Nieto says Mexico will not.
"Beginning today, the United States of America gets back control of its borders", the Republican president said.
Mr Trump's response has been to ask the US Congress to find between $12 and $15 billion (A$15 billion to A$20 billion) for construction and to help him find a way to recoup the money with some kind of tariff on Mexican imports. During the visit "to honor and remember the victims of the Holocaust, Foreign Secretary Dr. Luis Videgaray Caso expressed the affection of Mexico towards the people of Israel. I have no choice", Mr Trump said, marking a new low in US-Mexican relations.
Saturday night Netanyahu tweeted "President Trump is right".
Working out differences over trade and the controversial wall are part of "a comprehensive discussion on all aspects of the bilateral relationship", the White House and Mexico added.
The second order will strip federal grants from sanctuary cities - a term that usually refers to cities where local officials do not cooperate with federal immigration enforcement efforts that could lead to deportation.
Speaking to reporters Friday at a news conference with visiting British Prime Minister Theresa May, Trump said, "I have great respect for Mexico". "Defend the migrant Mexican workers, long live the immigrants!"