Twenty-five suspects are from Burundi and 16 from Gabon, a UN spokesman has said.
Last August, the UN envoy to CAR, Babacar Gaye, was sacked amid allegations of sexual abuse by troops.
Sexual abuse allegations against peacekeepers worldwide increased in 2015.
The UN has said there were 69 claims against military personnel, police and other staff in 2015, up from 52 in 2014 and 66 in 2013.
The UN had asked Burundi and Gabon to take "appropriate judicial action" against the 41 suspects, UN spokesman Stephane Dujarric said, AFP news agencies.
Under UN rules, it is up to the country that contributes the peacekeepers to investigate and prosecute any soldier accused of misconduct while serving under the UN flag.
The 41 suspects, who are not named in the report, were identified by victims through photographs or other evidence.
The alleged abuses took place in 2014 and 2015 in the Dekoa area in south-eastern CAR.
The UN investigation was carried out with the cooperation with of officials from Burundi and Gabon.
They interrogated 139 peacekeepers as they looked into complaints of abuse.
Last year, UN Secretary-General Ban Ki-moon called for "on-site court martial proceedings" for some crimes and a DNA database of all peacekeepers.
He also urged countries to change their laws so that they apply to sex crimes committed by citizens serving in UN peace operations.
A UN investigation has identified 41 peacekeepers as suspects in sexual abuse cases in the Central African Republic (CAR).