South Africa needed only 14.4 overs to reach their target of 172, with AB de Villiers making 71 in just 29 balls.
It gave them a 2-0 T20 series win to go with their 3-2 one-day series victory.
"The first half of the trip was very exciting," Bayliss said. "But we got worse as the series went on, and South Africa got better."
England won the four-match Test series 2-1 and took a 2-0 lead in the one-day international contest, before losing the final five fixtures on the tour (three ODIs and two T20s).
Their batting collapsed dramatically at the Wanderers, with seven wickets falling for 14 runs and the bowlers were then subjected to an onslaught from De Villiers and Hashim Amla, who took their team to 121-0 after just eight overs.
The South Africans struck 16 fours and nine sixes, with Amla unbeaten on 69 from 38 balls.
Such an emphatic defeat was ominous for England, who begin their ICC World Twenty20 campaign against West Indies in Mumbai on 16 March and face South Africa two days later.
"It's a bit of a reminder for people at home not to get too far ahead of themselves," Bayliss admitted.
"We have played some good cricket, but this is a young group of players and performances like this will happen from time to time."
The tourists changed their team for Sunday's match at the Wanderers, bringing in batsman Sam Billings for bowling all-rounder David Willey.
"In India we'll definitely be playing two spinners, so we just wanted to try having that extra batter, which we've done before, and just the five bowlers," Bayliss added.
Asked about the effects of a long tour he added: "I'm sure fatigue had a very small part to do with it, probably more mental than anything else. We've been away for five months apart from a week in between, when you count the UAE.
"But that's something these young players have got to get used to and if that's part of the learning curve for these young guys, there's something to learn from."
England skipper Eoin Morgan, who was run out at the non striker's end for 38, lamented: "Quite simply, we underperformed.
"The majority of our batting went really well - we were on course to get 185, 190, possibly 200.
"Myself and Jos Buttler were going really well, then we lost two wickets in two balls, and then from there we lost six wickets in the space of no time. I don't think we were too far behind the game, but the way we started with the ball allowed South Africa to get on top.
"The inconsistency is because we are inexperienced, and that is going to come. With that comes a great brand of cricket that is really exciting and can beat any side in the world."

The 27-year-old moved to Plainmoor in February and the club's current five-game unbeaten run has coincided with the five games that Racchi has started.
"He's got a great attitude, he wants to win, he wants everything badly because he's not been playing regularly for a few years," Nicholson told BBC Devon.
"He feels like he's got a point to prove and a career to save."
Racchi was released by National League North side Tamworth in December, having begun the season at Halifax.
Torquay are still three points from safety with a game on hand after a 0-0 draw with high-flying Braintree on Tuesday.
"He's been solid since he came here," added player-manager Nicholson, who has not featured in a league game since the Gulls' recent good form began.
"He's got a calming influence on the ball, that was one reason why I felt the time was right for me to come out of the team because I always like to see that as part of what I bring.
"Well Danny does that from the middle of the pitch now, so I can have dynamic full-backs now in the two that we've got and it's made a real difference."
England coach Trevor Bayliss admitted South Africa's nine-wicket Twenty20 thrashing of his team in Johannesburg was "men against boys".
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Torquay United midfielder Danny Racchi is "playing to save his career", says Gulls manager Kevin Nicholson.