Both sides were chasing a win after losing their opening fixtures in Group B, but an end-to-end match saw the two teams cancel each other out and effectively end their chances of progression.
Andre Anguissa opened the scoring in first-half stoppage-time as he raced onto a long ball from defender Michael Ngadeu-Ngadjui which exposed Australia's high back-line before poking the ball over the head of onrushing goalkeeper Mathew Ryan.
The lead was short-lived, however, as Alex Gersbach was brought down inside the area and Milligan despatched the spot-kick with precision after the video assistant referee (VAR) had ruled in favour of Australia.
Both sides wasted good chances to win the game late on, with the final result ultimately helping neither side in the quest for qualification from the group.
Australia made the more confident start on the back of a narrow 3-2 defeat to Germany and could have gone ahead in the second minute as Robbie Kruse shot tamely at Fabrice Ondoa.
Vincent Aboubakar looked threatening running in behind the Socceroos' defence and smashed a volley into the side-netting before hitting a free-kick into the wall as Cameroon grew into the match.
After threatening on the break, Cameroon finally took the lead as Ngadeu-Ngadjui hit a long ball into the right-hand channel and Anguissa escaped Milos Degenek enough to get to the ball first and fire a first international goal past Ryan.
Tomi Juric should have levelled minutes after the restart but fired over from six yards after being picked out by Mathew Leckie down the right, but his blushes were spared as Gersbach burst into the area before being felled by Ernest Mabouka.
VAR showed the original decision of the referee to be fair and Milligan stepped up to hit a precise penalty into the bottom-left corner to make it 1-1.
Aboubakar had a couple of chances to snatch the win late on, heading over from 12 yards before miscuing a half-volley with just five minutes to go as Cameroon looked to turn up the heat.
Tim Cahill, making his 99th appearance for Australia, was introduced in an attempt to change the game but he was starved of service as the wide men struggled to provide the quality as the game ended all square.
