Le Clos equalled Australian legend Ian Thorpe's record of seven medals in the Games, claiming the bronze medal in the 200m Individual Medley and bronze in the 4x100m Medley Relay.
The 22-year-old has now won 12 medals stretching over two Games which include the five medals from Delhi four years ago.
At the 2010 Commonwealth Games in Delhi, Le Clos won the 200m butterfly and the 400m individual medley, and collected silver in the 4x100m medley and two bronze medals in the 4x100m freestyle and 4x200m freestyle.
Le Clos claimed his fourth individual medal in Glasgow on Tuesday evening, finishing third in the men's 200m individual medley.
The Olympic gold medallist led from the start in his favourite butterfly stroke where he opened a comfortable lead.
The breaststroke leg, traditionally a weakness, saw Le Clos lose the lead and he had to hold on for third place in the freestyle leg as Australia's Daniel Tranter touched first in a Games record time of one minute, 57.83 seconds (1:57.83).
Scotsman Daniel Wallace claimed second in 1:58.72 with Le Clos bagging the bronze by the narrowest of margins in a time of 1:58.85 with Australia's Thomas Fraser-Holmes touching one-hundredth of a second behind him.
The 4x100m medley relay team of Le Clos, Cameron van der Burgh, Sebastien Rousseau, and Leith Shankland claimed South Africa's 12th swimming medal at the Games.
Earlier, South African swimming legend Roland Schoeman missed out on claiming his 13th medal as he ended his fifth and final Commonwealth Games.
The 34-year-old South African finished the men's 50m freestyle in fifth place behind winner 19-year-old Ben Proud, who clocked 21.92 seconds.
Australians Cameron McEvoy and James Magnussen took silver and bronze in 22 seconds and 22.10 sec respectively.
Schoeman, who uncharacteristically was only fourth off the blocks, never looked to be in the chase against the new order as he clocked a time of 22.36.
Games novice Brad Tandy finished seventh behind Schoeman in a time of 22.43 seconds.
Le Clos was South Africa's star performer at the Games with his two gold medals from the 100m and 200m buttterfly, 50m butterfly bronze, silver from the 4X100m relay and the bronze medal in the 4X200m relay.
World record holder Cameron van der Burgh, swimming in one of the most tightly contested strokes, relinquished his 100m breaststroke crown to England's Adam Peaty on Saturday to finish in second place.
Van der Burgh, however, demonstrated his resolve on Monday evening where he pipped the youngster to successfully defended his 50m breaststroke title in a new Games record time of 26.76 seconds.
The 23-year-old Sebastien Rousseau was also one of the standout swimmers for South Africa winning two individual medals with his 200m butterfly and 400m IM bronze medals.
He also featured in the silver-medal winning 4x200m relay freestyle team and Monday's 4x100m medley relay team to boast with four medals.
Rousseau featured in Tuesday's 200m IM final but could not add to his personal medal tally as he finish in eighth place in a time of 2:01.61.
Results from the eight swimming finals at the Commonwealth Games on Tuesday:
Women's 400m freestyle:
1. Lauren Boyle (NZL) 4min 04:47sec
2. Jazz Carlin (WAL) at 0:69
3. Bronte Barratt (AUS) 1:55
Men's 50m freestyle:
1. Ben Proud (ENG) 21:92sec
2. Cameron McEvoy (AUS) at 0:08
3. James Magnussen (AUS) 0:18
Women's 50m backstroke:
1. Georgia Davies (WAL) 27:56sec
2. Lauren Quigley (ENG) at 0:13
3. Emily Seebohm (AUS) 0:41
Men's 200m individual medley:
1. Daniel Tranter (AUS) 1min 57:83sec
2. Dan Wallace (SCO) at 0:89
3. Chad le Clos (RSA) 1:02
Women's para-sport 200m individual medley:
1. Sohpie Pascoe (NZL) 2min 27:74sec
2. Katherine Downie (AUS) at 4:24
3. Aurelie Rivard (CAN) 4:35
Men's 1500 freestyle:
1. Ryan Cochrane (CAN) 14min 44:03sec
2. Mack Horton (AUS) at 4:73
3. Daniel Jervis (WAL) 11:30
Women's 4x100m medley relay:
1. Australia 3min 56:23sec
2. England at 0:80
3. Canada 4:34
Men's 4x100m medley relay:
1. England 3min 31:51sec
2. Australia at 0:70
3. South Africa 2:96