The Florida Republican "appreciated receiving President Obama's phone call to discuss immigration reform late tonight in Jerusalem," Rubio said in a statement Tuesday issued by a spokesman.
Rubio, a Senate Foreign Relations Committee member and a possible 2016 GOP presidential hopeful, is touring Israel and Jordan.
"The senator told the president that he feels good about the ongoing negotiations in the Senate, and is hopeful the final product is something that can pass the Senate with strong bipartisan support," Rubio spokesman Alex Conant said.
The remarks came several hours after Obama phoned Rubio and fellow Republican Sens. Lindsey Graham of South Carolina and John McCain of Arizona -- three of the four GOP members of a Senate bipartisan group of eight seeking to create a legislative compromise on overhauling the nation's immigration system.
In the phone calls, Obama discussed with the senators "their shared commitment to bipartisan, common-sense immigration reform," the White House said.
Obama also commended the senators "for the bipartisan progress that continues to be made by the Gang of 8 on this important issue," the White House said.
The fourth Republican member of the group, Sen. Jeff Flake of Arizona, was in Cuba with a seven-member bipartisan congressional delegation. The White House said Obama hoped to talk to him soon.
"During the calls, which build on conversations that have taken place at the staff level, the president reiterated that he remains supportive of the effort under way in Congress, and that he hopes that they can produce a bill as soon as possible that reflects shared core principles on reform," the White House said in a statement.
GOP lawmakers have complained Obama had not reached across the aisle on the bipartisan Senate group but met with Democrats last week.
"As the president made clear when he met with Democratic senators involved in the process last week, that while he is pleased with the progress and supportive of the effort to date, he is prepared to submit his own legislation if Congress fails to act," the White House statement said.
A leaked White House draft immigration plan -- which includes an eight-year pathway to citizenship for illegal immigrants and makes no mention of border-security triggers most Republicans favor -- prompted angry Republican comments over the weekend.
Rubio Saturday called the plan "half-baked and seriously flawed" and said it "would be dead on arrival in Congress" if it were ever proposed.
The White House insisted over the weekend, and again Monday and Tuesday, the leak to USA Today late Saturday was not intentional.
A White House official told The Wall Street Journal Sunday administration officials reached out to Democratic and Republican Senate offices Saturday night to make that clear.
The White House earlier circulated the draft to federal agencies for comment, which meant numerous government officials had seen it, the Journal said.