Cordina, 31, stripped of the belt due to injury last year, became the first Welsh boxer to become a two-time world champion, but was made to dig deep in a classic encounter in front of his home fans.
One of the judges’ score cards had Rakhimov as a 116-111 winner, while two others gave Cordina the verdict with scores of 115-112 and 114-113 in his favour.
Now undefeated in 16 professional fights, Cordina sent Rakhimov to the canvas in the second round and after being hurt badly himself in the fifth, produced a rousing finish in the final round to edge a classic.
Tajikistan’s Rakhimov, 28, who had won 17 and drawn one of his previous 18 fights, was unrelenting despite fighting with a closed right eye from the sixth round.
The champion threw a greater quantity of punches in his first title defence since winning the belt by stopping Manchester’s Zelfa Barrett last November, but Cordina produced more accurate, quality shots.
Cordina displayed superb footwork in the opening round as the champion forced the issue, but the Welshman cut loose in the second, sending the champion to the canvas with a shuddering left hook.
Rakhimov beat the count and despite looking shaky on his legs, he recovered from successive right upper and left-hook combinations to jolt the challenger with a solid right.
Both boxers maintained a furious pace. Cordina caught Rakhimov with a booming left hook in the fourth round, but was in trouble himself in the fifth after being stunned by a booming right.
Rakhimov, fully recovered from his knockdown, continued to be the aggressor in the sixth, but was hindered by a badly swollen right eye and was visibly hurt again by Cordina’s combinations.
The champion’s knees were buckled again in the 10th, but he showed tremendous resolve to keep Cordina on the back foot, but the British fighter landed more punishing blows in the final round to clinch it.
Cordina, now undefeated in 16 professional fights, first won the title in Cardiff in June last year when knocking out Japan’s Kenichi Ogawa at the Motorpoint Arena in the second round.
He was scheduled to defend his title against mandatory IBF challenger Rakhimov in November, but was forced to pull out due to a hand injury and was subsequently stripped of his belt.