At the close, West Indies were 178 for one in reply to South Africa's 532, with Gayle undefeated on 112 and Ramnaresh Sarwan 39 not out.
The left-handed Gayle reached his century off just 79 balls, crashing 19 fours and a six as he raced to three figures and also past 2,000 runs in Tests.
His achievement at Newlands was all the more extraordinary in that he was still recovering from a torn hamstring that almost kept him out of the match.
"When I was batting, I really didn't think of my injury," Gayle said. "I was scoring freely but I was trying to keep my composure as well. It paid off for me.
"So far it's been a great innings but I'd love to go on and get an even bigger one tomorrow."
The 24-year-old Jamaican celebrated his hundred after a rare scampered single, jumping in the air before doing a little jig on his injured leg.
When he reached three figures, his opening partner Daren Ganga had scored just 17. Ganga departed without adding to that, bowled off the inside edge by Andre Nel with West Indies on 126.
Sarwan also scored at a good pace in the final hour but never came close to reproducing the phenomenal fireworks of his team mate, who had faced 105 balls by the close.
In all, 402 runs were scored on the day, including 20 fours and a six by Gayle.
WINDIES FRUSTRATION
Earlier Mark Boucher struck an undefeated 122,
Boucher was aggressive, although not without some good fortune.
On 15, he was clean bowled by a yorker from Fidel Edwards and, on 59, substitute fielder Carlton Baugh failed to hold on to a stinging chance at backward point off Vasbert Drakes.
By the time Nel was caught behind off Adam Sanford for four to end the innings, Boucher had spent a little over four hours at the crease, facing 173 balls and hitting 21 fours.
Any realistic chance West Indies had of winning the Test match and squaring the series drifted away during a partnership of 146 for the eighth wicket between Boucher and Jacques Kallis, a record for South Africa against West Indies.
Kallis resumed his innings early on the second day having retired hurt after being hit on the elbow by a bouncer on Friday.
When he was dismissed it was in controversial fashion. Kallis made no attempt to hide his disappointment when umpire Daryll Harper upheld an appeal for lbw from Sanford, although television replays suggested the ball would have passed over the stumps.
Kallis made 73 in three and half hours, facing 145 balls and striking 13 boundaries.
Boucher and Ntini then shared 52 for the ninth wicket before Ntini was given out caught behind off wrist spinner Dave Mohammed for 18.
