Hayatou used his re-election at the organisation's congress in Marrakech in Morocco to take a swipe at rival Jacques Anouma, who was disqualified from the contest despite several attempts to get his name on the ballot.
"The presidents of the federations approved an amendment preventing a few of them from participating in the race for the CAF presidency, which now permits only those who have held positions of responsibility within the institution to run for presidency," Hayatou told delegates.
"The conduct of the Executive Committee along with the members of national associations during this case was exemplary. The principle of sovereignty of the General Assembly was recognised by the Court of Arbitration for Sport."
Hayatou last year steered an amendment through a specially convened congress to prevent all but executive committee members from running for the presidency, thereby excluding Anouma from the race.
It was overwhelmingly adopted despite the fact most voters were ruling themselves out of a chance of standing for the top post.
Anouma - who then had two bids to overturn the decision rejected by the Swiss-based CAS - was conspicuous by his absence at the congress, where the 66-year-old Hayatou celebrated a further four-year term, which means he will have had 29 years in charge when it runs out in 2017.
His re-election was hailed by FIFA president Sepp Blatter.
"Congratulated Issa Hayatou for 25 years of CAF presidency and reelection today. A great and committed football leader," the head of soccer's world governing body wrote on Twitter.
While his re-election was a mere formality, several hotly contested polls for executive committee seats were scheduled to be decided on Sunday as the congress ran over its scheduled lunch time close.