Officials said the two countries agreed on the text of an agreement, which now has to be reviewed by government agencies in Bogota and Washington before getting a final signature.
But the move, coming after Ecuador refused to renew an agreement allowing the US military to fly out of Manta for the past 10 years, has drawn angry reaction from governments across Latin America.
Hugo Chavez, the Venezuelan president, led the attack along with Rafael Correa, his Ecuadoran counterpart and ally.
Speaking in Quito, the Ecuador capital, at a recent regional summit, Chavez said he was fulfilling his "moral duty" by telling fellow leaders that the "winds of war were beginning to blow".
"This could generate a war in South America," he said.
However, Frank Mora, a US defence department official for Latin America, dismissed the controversy as a tempest in a teapot.
"This agreement simply formalises what already almost exists right now," he told the AFP news agency.
A senior US military officer said on Thursday that the US needed to reassure regional powers about the deal.
"I think we need to do a better job of explaining to them what we're doing and making it as transparent as possible, because anybody's concerns are valid," General James Cartwright, vice-chairman of the US joint chiefs of staff, said.
Cartwright and Robert Gates, the US defence secretary, also said the deal was not a unilateral move but the product of a partnership with Colombia designed to target drug cartels.
"The strategic intent is, in fact, to be able to provide to the Colombians what they need in order to continue to prosecute their efforts against the internal threats that they have," Cartwright said.