Manyama netted one more goal than Orlando Pirates hitman Tendai Ndoro, who started the campaign in blistering fashion but ran out of steam as the campaign progressed.
No other players hit double figures in the Premiership, with Bidvest Wits' Gabadinho Mhango and Polokwane City's Rodney Ramagalela next best on nine strikes apiece.
Mamelodi Sundowns pair Khama Billiat and Themba Zwane scored eight times in the league, as did SuperSport United's Jeremy Brockie and Chippa United forward Rhulani Manzini.
Highlands Park's Collins Mbesuma won last season's Golden Boot with 14 goals when in the colours of Mpumalanga Black Aces.
Past 16-team PSL League top scorers:
2016/17: Lebogang Manyama - 13
2015/16: Collins Mbesuma - 14
2014/15: Moeketsi Sekola - 14
2013/14: Bernard Parker - 10
2012/13: Katlego Mashego - 13
2011/12: Siyabonga Nomvete - 20
2010/11: Knowledge Musona - 15
2009/10: Katlego Mphela - 17
2008/09: Richard Henyekane - 19
2007/08: James Chamanga -14
2006/07: Chris Katongo - 15
2005/06: Mame Niang - 14
2004/05: Collins Mbesuma - 25
2003/04: Jackie Ledwaba - 14
2002/03: Lesley Manyathela - 18