Burnham outclassed Otago University 36-26 in the final at the University Oval on Saturday.
It was the first time the cup had left Otago since University won it off Southland club Ohai-Nightcaps in 1990.
The Middlesex Cup was first contested in 1951 and has crossed Cook Strait 17 times, but this was the first time it had been won by a Canterbury club.
McGoon played aggressively and the student defence was not able to stop him when he accelerated at full throttle.
His first try, after three minutes, rocked the students' confidence and helped Burnham to a 17-7 lead at the break.
He added two more in the first three minutes of the second spell to stretch the lead to 31-14 and take the cup out of the students' grasp.
Hugh Blake scored two tries for Burnham with his elusive running and a sixth try went to teenager Nela Manu, the younger brother of Highlanders No 8 Nasi Manu.
Matt Faddes used his speed to score the first try of the game and was the best University back.
Brad Cameron was aggressive on defence and scored an early second-half try to keep the students in touch.
University beat Dunedin 24-14 in one semifinal, and Burnham beat Green Island 31-12 in the other.
Alhambra-Union won the bowl when it beat Pirates 34-5, and the Otago Daily Times Cup was won by Southern, when it beat Taieri 25-19 in extra time.
Pirates beat University three games to none in the women's competition.
