Trek-Segafredo rider Porte trailed Mitchelton-Scott’s Daryl Impey coming into the last stage but a late attack from a big breakaway saw the Australian power away from his rival.
Impey was unable to keep the pace and ended up coming in a total of 30 seconds down on Porte as the general classification changed hands at the end.
It is Porte’s second win after he triumphed in 2017, with Impey winning each of the last two years.
"To win the race again is a fantastic feeling," said Porte.
"It was a hard day for our team; there were times when I thought maybe the GC was over and done with because it was a big group up the road. But credit to the guys, almost single-handedly, they brought that all back.”
Holmes takes first professional victory as Porte wins GC
World champion Mads Pedersen drew some attention as he came last but Porte was quick to point out the work the Dane was doing for him.
"You know people are quick to single out Mads Pedersen because he's the World Champion here helping me, but every one of my team-mates has been incredible; they all played their part in today.
"The boys were fantastic all week; I tip my cap to them. It was a little bit panic stations there in the middle, we had to ride hard for the whole day, and AG2R also helped.
"Mads (Pedersen) pretty much single-handedly took two minutes out of the 26 guys up the road. He's a fantastic guy. When he won the Worlds, a few days after, he said to me that he would come down to Tour Down Under and help me to try and win the race. For him to back that up …he's been awesome, all week, like all the guys have. We have new team-mates in two young neo-pros and Kenny Elissonde as well and they all stepped up, so a big credit to them. It's a great feeling to finish their work off this week."
Despite the overall race win, it wasn’t to be Porte’s seventh consecutive stage win at the top of Willunga Hill, as Great Britain’s Matt Holmes kept pace with the race winner and took the stage win for his own.
Holmes wasn't worried about peloton
"I wasn't really thinking about the gap," 26-year-old Holmes said about the latter stage of the race after his first professional win.
"I was just thinking about the group I was with, and I thought there was no way I would win from that situation; it was such a good group.
"I've never really raced up a climb. I've been stuck in Britain for the last six years, which is not a bad thing. This is my second hilltop finish this week, and it seems to suit me."