Pence later met with Caribbean leaders before departing Lima to return to Washington.
Despite Trump's absence, USA officials sought to use the summit to counter China's rising influence in Latin America and condemn Venezuela's government.
Trump and Pena Nieto have yet to meet in person since Trump became president previous year.
Pence is departing for the Summit of the Americas in Lima on Friday.
"I reiterate the call to make a regional pact against corruption", said Peru's President Martín Vizcarra in front of leaders from the region.
The United States, France and Britain were all taking part in the strikes against Bashar al-Assad's Syrian regime.
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But he said it was "intellectually bankrupt" to expect the security services to lay out all the information they have. There have been calls from opposition parties and some Conservative MPs for Parliament to have a vote beforehand.
US Vice President Mike Pence abruptly skipped an official banquet in Peru late Friday ahead of a summit with Latin American leaders, as President Donald Trump announced he had ordered air strikes on Syria.
Sixteen countries at the meeting issued a declaration calling for transparent elections in Venezuela and on worldwide organizations to "immediately implement a program of humanitarian assistance". Pence's deputy chief of staff, Jarrod Agen, told Reuters he planned to discuss the strikes in his speech on Saturday and in meetings with leaders.
President Donald Trump has partially rolled back former President Barack Obama's diplomatic opening with the communist island.
"The Lima Summit was the beginning of the end of the Summit of the Americas", he added from the presidential palace in Caracas where he had met with Bolivian President Evo Morales.
According to the US State Department, the United States is providing $16 million in extra funding for humanitarian assistance for Venezuelans who have fled as economic conditions worsen.
"Canada stands with our friends in this necessary response, and we condemn in the strongest possible terms the use of chemical weapons in last week's attack", Canadian Prime Minister Justin Trudeau told the gathering of regional leaders.
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"There's deep concern in Brazil with the escalation of military conflict in Syria", Brazilian President Michel Temer told the summit.
Pence, who is representing the United States at the Summit of the Americas in place of President Donald Trump, said he hoped that the military action, which also involved France and Great Britain, would cause Syria "and their patrons in Russian Federation and Iran" to abandon "the use of chemical weapons against innocent civilians".
President Nicolas Maduro was barred from attending the summit his aims to put on a presidential elections that a sham is considered by lots of governments and that the opposition is boycotting.
Mexico also is taking part in a renegotiation of the North American Free Trade Agreement with the USA and Canada due to demands for changes from Trump. Pence is subbing for President Donald Trump after the president pulled out of his first planned visit to Latin America to manage the United States response to an apparent chemical weapons attack on civilians in Syria.
The Summit of the Americas has lost legitimacy in the face of the peoples of the region, stated the Argentinean intellectual Atilio Boron, in an interview granted to Telesur in this capital.
In a series of meetings with Latin American leaders, Pence plans to promote good governance and democratic institutions and urge allies to maintain pressure on Maduro.
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