Jacques Kallis (51) and Ashwell Prince (59 not out) steered South Africa to a 2-1 series win after coming together when their side were wobbling at 39 for four in their quest for a target of 161 on a tricky pitch.
They put on 117 for the fifth wicket before Kallis was bowled by Shahid Nazir when just five runs were needed for victory.
Kallis and Prince had to work hard while opening bowler Mohammad Asif and leg-spinner Danish Kaneria bowled superbly in tandem.
"They put us under a lot of pressure and we just had to absorb it," said Kallis.
"But there is no way you can carry on doing it all day and there had to come a period where they would crack and perhaps start trying a few things. It happened after lunch and once we got the momentum things became a lot easier."
Pakistan's problem was that their other bowlers could not maintain the standard set by Asif and Kaneria, especially with Mohammad Sami having split the webbing of his bowling hand while fielding Saturday.
Woolmer pointed out that three of his leading bowlers were back in Pakistan. "The current schedules are ridiculous," he said.
"You are already seeing players like Shaun Pollock and Makhaya Ntini who are exhausted and today Asif was an example. Fatigue leads to injuries. It's a proven equation. If you have too much fatigue, your back goes or you twinge a hamstring or get a stress fracture.
"Cricket has to look at it. As a coach I have to manage these things. We've got Umar Gul, Shoaib Akhtar and Shabbir Ahmed sitting at home. Somewhere along the line the commercial aspects and the physical aspects of looking after players have to be revisited."
Pakistan captain Inzamam-ul-Haq was off the field for much of the final day with a back injury. "We don't know the severity of it yet but he couldn't bend down so he came off the field. He's had the same injury before," said Woolmer.
He said it was too early to make a call on the likelihood of Inzamam being fit for a five-match one-day series which starts next Sunday following a Twenty20 international in Johannesburg Friday.
Woolmer said the series loss was disappointing but he said it showed Pakistan had improved since losing all three Tests of a series in Australia two seasons ago on similar, bouncy pitches.
Asif took two early wickets, dismissing South African captain Graeme Smith and Hashim Amla, to put the home side under pressure.
When Asif was rested half an hour before lunch he had bowled a spell of 11 overs in which he took two wickets for six runs, while South Africa had advanced by just 18 runs in 22.5 overs from their overnight total of 36 for two.
"Asif has been incredible," said Woolmer. "He's a top quality bowler. He's still young in Test cricket and has got a long way to mature but he's very close to the top of his trade already.
With fine tuning and greater fitness levels he'll be a real force in the future of Pakistan cricket."
South African captain Graeme Smith gave credit to Pakistan for providing a highly competitive series. "They performed very well. On all their trips to South Africa these wickets probably were the closest to what they've got back home. They made life difficult for us."
Smith said Kallis and Prince had shown their quality. "On a wicket like this it is where your big pressure players come to the party and make the impact that's needed."
Kallis said: "Sometimes you get more pleasure out of knocks like this than getting a hundred, because it played a big role in winning the game for South Africa which to me is more important than getting a hundred."
Asif struck with his fourth ball of the morning when Smith advanced down the pitch and tried to force him to the leg-side, missing the ball to be given out leg before.
Hashim Amla was caught behind off Sami four overs later for three.
There was some vociferous appealing, particularly early in the day, and at one stage umpires Peter Parker and Steve Bucknor spoke to acting captain Younis Khan, warning the players to 'keep down the banter.'
"It was nothing out of the ordinary," said Kallis. "It was a hard series. It was hard cricket and there were tense moments but that's what Test cricket is about. It's what our guys like and it brings the best out of quite a few of our players."
There was an incident shortly before the end of the match when Kaneria, fielding on the boundary, reported a spectator who allegedly swore at him.