Scotland needed to win by two goals at Wembley for the first time in more than 50 years to deny England.
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However the victory may serve to ensure Brown is allowed to see out his contract, which runs for another two years.
Anything less than this epic performance from the battling Scots would have stoked the growing calls for his resignation.
As it was, his players have appeared to have silenced them.
"My contract expires in December 2001 and I intend to honour it," he said.
"All this stuff about my contract and my position between these two matches has been very unnecessary. The players have been very supportive, not that I asked them to be.
"People should remember we don't lose many games and have never lost two successive competitive matches and we have a habit of scoring away from home.
"I feel really gutted that we failed to qualify for Euro 2000. It is a major disappointment and I feel very upset.
"I felt that we didn't have any breaks in the two games and I couldn't have asked for anything more from my players."
The Scots were denied the extra-time they deserved by England keeper David Seaman.
The Arsenal keeper pulled off a fantastic penalty save when the sides last met in Euro 96 and made a point blank stop from Christian Dailly.
Brown said: "He certainly raises his game when he plays against us."
Both Kevin Keegan and Tony Adams took time at the end of the game to seek out the Scotland boss.
Keegan told Brown that his team had been magnificent while Adams ran 50 yards to relay a similar message.
Brown saluted his players, saying: "I'm proud of these guys tonight I got a great response from all the players."
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We've a long way to go - Keegan
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Sorry England scrape into Euro 2000
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England v Scotland - picture gallery
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Watch out Scotland, warns Becks
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Scotland squad guide
England squad guide
Great border skirmishes
Generals in the firing line
A history of fierce football rivalry
Fans in court over football trouble
Scotland v England
Lambert out of play-offs
Hendry's double jeopardy
Brown cautious over Hendry injury
The limitations of passion-play
England claim the prize
All quiet after Wembley showdown
Timeline: England v Scotland II
Hooligans face up to smart cameras
Cheers and tears for Scotland