Bozize fled to Cameroon after rebels seized control over the CAR capital last month. The rebels have dissolved the constitution, called for new elections in 2016 and installed leader Michel Djotodia as president.
Bozize told the BBC that CAR forces had "neutralized" Seleka fighters, who were later supported by "Chadian special forces" in the takeover.
Bozize said he resigned to avoid more bloodshed.
"We had a solid and friendship relation with the Chadian authorities," he said. "Chad alone can give an explanation."
Chad didn't comment to the BBC on the allegations. The government there is hosting an emergency summit on CAR and rebel leaders sent Prime Minister Nicolas Tiangaye to the meeting.
African and Western leaders condemned the Seleka takeover. The U.S. State Department described the incident as an illegal seizure of power by force, but stopped short of characterizing the incident as a coup.
"The legal definition of coup involves the military of the country, the constituted military of the country, overthrowing the government," State Department spokeswoman Victoria Nuland said. "In this case, we have a rebel organization overthrowing the government."