Three years later in England, his talented South African side wept after they tied their epic semi-final against eventual champions Australia and bowed out on inferior net run-rate.
Woolmer never forgot those setbacks, but he acknowledged that the challenge of coaching Pakistan, one of the most volatile teams in world cricket, was taking its toll.
After his side crashed out of the World Cup last weekend in Kingston against debutants Ireland, Woolmer hinted at the strain he was under.
"Cricket is a game where anything can happen and nothing should ever be taken as granted"
Bob Woolmer, former Pakistan cricket coach
"Doing it internationally, it takes a toll on you - the endless travelling and the non-stop living out of hotels," he said.
After being found unconscious in a Kingston hotel on Sunday, he died in hospital.
Jamaican police announced on Thursday that he was strangled to death, and a murder investigation has been opened.
The 58-year-old was driven by a desire to land the ultimate prize in the game.
He said on the eve of the tournament in the Caribbean: "It is always disappointing as a team not to achieve the ultimate goal, but it was not for the lack of trying.
"Cricket is a game where anything can happen and nothing should ever be taken as granted."
After leaving the South Africa job, a two-year stint as the International Cricket Council's High Performance Manager allowed Woolmer to work with fledgling cricketing nations like Kenya, Namibia and the Netherlands during the 2003 World Cup.
Fate brought him in 2004 to Pakistan as coach, regarded as the south Asian country's hottest sports post which had seen five changes since 1999 before his arrival.
He forged a strong relationship with captain Inzamam-ul-Haq and saw to it that the skilful cricketers always remained strong in basics.
Woolmer believed that Pakistan had been moving in the right direction.
"There are completely different dynamics with the Pakistan team from that of South Africa. I have enjoyed coaching them," he said.
Born in the Indian city of Kanpur in 1948, Woolmer played 19 Tests for England in the 1970s but missed the inaugural World Cup in 1975 due to injury.
"I broke my left hand so I was left to do the 12th man duties," recalled Woolmer, whose career ended prematurely as he first joined Kerry Packer World Series Cricket and then went on tours to South Africa in the 1980s.
He steadily developed into a well-respected coach, and was credited with pioneering the use of computers in cricket.
His creative and adventurous ways helped South Africa become a formidable team which started the 1996 World Cup as one of the favourites.
"We had a good plan in 1996, but were undone by a great performance by [century-maker] Brian Lara in the quarter-final," said Woolmer, under whom South Africa won the inaugural Champions Trophy in 1998 and were hot favourites for the 1999 World Cup.
"It was cruel to lose by a run-rate of 0.01 which was the closest of margins. It was very depressing."
The series of events over the last seven months led to an implosion in Pakistan cricket and added to Woolmer's stress.
Last August, Woolmer's team was engulfed in a ball-tampering row which led to them forfeiting the final Test against England at The Oval, the first time in the history of the game that a match had ended in such a controversial manner.
Woolmer's planning for the World Cup was then sent into complete disarray when his two best fast bowlers, Shoaib Akhtar and Mohammad Asif, failed drugs tests and were suspended.
They had their bans controversially lifted but then missed the World Cup due to injury.