"Our crew kept an eye on them and reported back to the Police Maritime Unit and Coastguard as well as their location and condition,'' a police statement said.
The Coastguard and Westpac Rescue Helicopter were also sent, police said,but officers on the Eagle soon noticed the condition of one of the kayakers deteriorating.
"The guy who was still in the water had started to turn blue and was struggling to hold on to the kayak, so one of our rescue swimmers was sent into the water."
The police officer stayed in the water with the pair for between 10 to 15 minutes before Coastguard arrived at the scene.
The kayak had flipped shortly before Coastguard got there; allowing the officer to get both kayakers back on to the vessel.
All three were taken to Cornwallis wharf where paramedics tended to them.
Sergeant Callum Young, of the Air Support Unit, praised the officer for his efforts as although they are called out to water rescues regularly, it was rare for one of their crew to have to jump into the ocean.
"It was great work by the Eagle crew and especially the officer who jumped into the water.''
Young also praised the two kayakers, who he said had done everything right and had been wearing life jackets at the time.
But choppy conditions had been a key factor in the incident.
"The incident highlights the importance of water safety and being prepared for rapidly changing conditions.
"It could have been a very different outcome if they hadn't been wearing life jackets,'' he said.
As well as the Coastguard, the Westpac Rescue Helicopter also assisted in today's rescue.
