Ali's spin skittled out the opponents for 187 runs on the last day of the last warm-up game as the home side offered scant resistance after resuming on 35-2, 243 runs behind the tourists who had proven rampant with the bat on the second day at the City Oval on Monday.
England declared on 414 for six in reply to the home side's first innings tally of 136.
Ali finished with figures of six wickets for 77.
Seamer Steven Finn took two quick wickets to add to the four he took in the first innings and should be enough to earn him a place in the England side for the first test against South Africa, which starts in Durban on Saturday.
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England began on Tuesday with a wicket with their first ball as Mark Footitt, also fighting for a test place, had night watchman Marchant de Lange caught at short leg by James Taylor.
After test players Quinton de Kock and Rilee Rossouw put on 67 runs for the fourth wicket, Ali made a breakthrough by trapping De Kock leg before wicket for 53 and Rossouw not long after in a similar fashion for 32.
Finn then took two wickets in a single over as South Africa A slumped to 110 for seven.
The last three wickets fell to Ali with wicketkeeper Dane Vilas, dropped by South Africa after the recent test defeat in India, unbeaten on 30.
(Reporting by Mark Gleeson in Cape Town; Editing by Sudipto Ganguly; mark.gleeson@thomsonreuters.com; +27828257807; Reuters Messaging: Reuters Messaging: mark.gleeson.thomsonreuters.com@reuters.net)
