The shock result leaves Italian 13th seed Fognini facing unseeded Serb Dusan Lajovic in Sunday's unscripted final.
The runner, participating in his fourth half marathon, collapsed in the race on Saturday.
The Brumbies defended as a unit, making over 200 tackles – three times more than the Stormers – while they also forced 10 turnovers against a hapless Cape side.
But City’s 10th Premier League in a row came at a price with key midfielder Kevin De Bruyne forced off with what looked like another knee injury in the 38th minute.
Steve Smith, who along with compatriot David Warner missed the 2018 IPL because of the scandal, will replace India's Ajinkya Rahane.
Liverpool defender Virgil Van Dijk joins team-mate Sadio Mane on the list, while City forward Raheem Sterling is included alongside team-mates Sergio Aguero and Bernardo Silva.
Neymar, who has scored 13 goals from 13 league appearances this season, has been out of action since picking up a foot injury in January.
In the women’s Ultra, Steyn defended her title in a time of 3:31:28 seconds. Another South Africa Irvette van Zyl rounded off the podium in third.
Klopp said his players have benefited from the experience of reaching the Champions League final as well as securing a Premier League top-four finish last year.
City’s quadruple bid ended when they went out of Europe on the away goals rule on Wednesday, despite winning 4-3 win at the Etihad Stadium, after the two-legged quarter-final tie finished 4-4 on aggregate.
