Pakistan were dismissed for 145 in their second innings in 13 minutes of play on the fifth day, and then captain Mark Taylor gave England a warning for the winter's Ashes series.
The 28-year-old MacGill originally came into the Australia side as a replacement for Shane Warne, recovering from major shoulder surgery. Now he wants to form a partnership with the Australian spinner.
He said: "It is pleasing to perform like this and a great thrill. I look forward to bowling with Shane in the time to come and it will be an honour for me."
And the Australian captain admitted there could be a MacGill-Warne spin spearhead against England from next month.
Taylor said: "MacGill got a chance and he grabbed it with both hands. He has taken 14 wickets in just two Tests and it will be great to have him alongside Warne in the Ashes."
MacGill bowled alongside Warne during his Test debut against South Africa in Adelaide in 1997-98. He took five wickets in that match. But with Warne still battling for fitness, the Australian selectors could face a difficult choice if only one spinner is needed in any of the Ashes matches.
Warne, who has 313 wickets in 67 Tests, sent a congratulatory fax to MacGill on his first innings five-wicket haul. MacGill said: "He has been very courteous and helpful. It was a kind gesture and it spurred me on."
As a child, MacGill had wanted to emulate Australian paceman Dennis Lillee, who was a close friend of his father. MacGill would watch his father bowl leg-spin and Lillee's pace for Western Australia, but his physique did not allow him to become a fast bowler.
Of the Test victory, Taylor said: "It's a fantastic feeling. Having won Tests in the West Indies, South Africa, New Zealand and India we were aspiring for a win here and that has come after 39 years."
It was Australia's first win in a Test in Pakistan since 1959-60 when Richie Benaud's team routed Pakistan 2-0 in a three-match series.
Australia, on their subsequent five visits to Pakistan, failed to win a single test. Taylor, whose first match as captain was in Karachi in the 1994-95 series, has now won 23 of his 43 Tests. He lost his first series in Pakistan 1-0. MacGill finished with 9 for 113 (5 for 66 and 4 for 47) in only his second Test. And Taylor also praised his batsmen, who rallied from 53-3 at lunch on Friday to 513 all out.
He said: "The batsmen did well to come out of a collapse. Slater, Steve Waugh, Healy batted superbly as did Lehmann. And the bowling was good. MacGill bowled accurately and was supported by McGrath, Fleming and Miller. We are happier even more because of Healy reaching a landmark of 356 dismissals behind the wicket to create a new world record. He is a superb team man."
The final day's play in the first of a three-test series was a formality as Pakistan resumed at 137 for 9, trailing by 107 runs on the first innings. Salim Malik was 48, Saqlain Mushtaq was three.
In the fourth over of the day Saqlain was leg before to Glenn McGrath for seven but not before his partner Salim Malik had reached his 29th test fifty.
Malik took two runs off McGrath to reach his fifty, but it was a vain attempt to keep the Australians at bay.
Fourth day; Pakistan won toss
Australia win by an innings and 99 runs
PAKISTAN - First innings 269 (Saeed Anwar 145; SCG MacGill 5-66).
AUSTRALIA - First innings 513 (SR Waugh 157, MJ Slater 108, DS Lehmann 98, I Healy 82).
PAKISTAN - Second Innings
Overnight (Pakistan 137-9, Salim Malik 48*)
Saleem Malik not out 52
Saqlain Mushtaq lbw McGrath 7
Extras: (3lb) 3
Total: (all out, 75.5 overs) 145
Bowling: McGrath 16.5-6-24-2 Fleming 15-4-38-2, Miller 21-8-30-2, MacGill 20-7-47-4, Lehmann 3-2-3-0.
Umpires: Javed Akhtar and P Willey.
Man of the Match: S R Waugh.Reuse content