Cotton, who blasted the Hawks for 45 to clinch last year's grand final series, was back to his blistering best, connecting on 7/11 threes.
The Cats also received a strong contribution off the bench from Derek Cooke Jr (19 points, seven rebounds), while JP Tokoto finished with 13 points after having just two at half-time.
Acrobatic Illawarra import Demitrius Conger returned with a bang after a one-game suspension, pouring in a team-high 30.
But the reigning champions absorbed the Hawks' best punches for three quarters before pulling away down the stretch and joining New Zealand at the top of the ladder with a 10-3 record.
The Hawks slipped to 5-8 but will be comforted by the fact their next six games are in Wollongong.
Kevin White moved back into the starting five to cover the absence of injured guard Mitch Norton and helped the Hawks jump out to a 13-8 lead.
But Cotton signalled his intentions by nailing his first four shots, as the 'Cats peeled off a 12-2 run.
Illawarra coach Rob Beveridge held his breath when AJ Ogilvy went down injured after six minutes. The three-time All-NBL centre headed to the locker room before returning to the court in the second period and finishing the game with 10 points and eight rebounds.
Luckily for the Hawks, Conger was cooking from the get-go, racking up nine points and three boards in the first quarter.
Cotton nailed a pair of free throws in the closing seconds to give the visitors a 25-24 quarter-time lead.
Illawarra gave Cotton less room to operate in the second period, allowing him to add just four to his tally.
Conger upped his total to 14 by half-time and Clarke had 10, which included a long-distance bomb and a dazzling reverse layup.
The 'Cats were slapped with two technicals in the first half and Tokoto was uncharacteristically cold, missing seven of eight shots and racking up three fouls and three turnovers.
But Perth got timely help from the bench with Cooke Jr's 10 points and four rebounds, taking a 46-44 lead into the main break.
Cotton kept the 'Cats in front with a couple of early threes in the third period, though it didn't stop coach Trevor Gleeson using a timeout after one too many defensive lapses.
He got the response he was after, as Perth knuckled down at both ends to pull ahead 71-64 at three-quarter time.
They kept the Hawks at bay down the stretch to stay on track for the minor premiership.
PERTH WILDCATS 99 (Cotton 36, Cooke Jr 19, Tokoto 13)
ILLAWARRA HAWKS 91 (Conger 30, Clarke 12, Kay 11