The wing-back will join Fleetwood Town, becoming the new manager’s first recruit on the Fylde coast, upon expiry of his deal in Perth.
Rooney leaves McDiarmid Park a club legend having scored in both the Scottish Cup and Betfred Cup wins last year during the Saints’ unprecedented silverware double. He also helped keep the club in the cinch Premiership by finding the net in the 4-0 play-off second-leg win over Inverness.
Now he will link up with Brown during his first managerial role at the Highbury Stadium having turned down an offer to stay in Perth.
Rooney said: “I thoroughly enjoyed my two seasons at St Johnstone. They have been the happiest and most successful of my career. The memories of scoring in both cup finals will never leave me. The pleasure it gave the St Johnstone supporters was an absolute privilege and an honour for me.
“To round it off by scoring our fourth goal on Monday night will be unforgettable.
“However, I want to try my luck down south once again and Fleetwood Town are giving me the opportunity to do so.
“I would like to wish the gaffer (Callum Davidson), the coaching staff, Liam Gordon and the squad, the Board and supporters all the very best for the future.”
Brown said Rooney, who has previous experience in England with York City, brings “a lot of quality defensively and going forward”.
He told his new club’s website: “I’ve played against him many times and know he’s a real winner who has determination and will put his body on the line for the team.
“Shaun can play in a few different positions and he’s a great addition to the squad. From my point of view to have my first signing a player who I know so well is a big plus for me.”
Saints boss, Callum Davidson said: “We wish Shaun all the best at Fleetwood Town. He has played a huge part in what has happened at this football club the last two seasons and he gave his all in every game. As a manager, we can’t ask for any more than that.”