World champion Thorpe, who retained his 400 freestyle crown on Saturday, drew first blood in his first head-to-head with Phelps on Sunday, leading all the way to win their semi-final clash in one minute 46.65 seconds.
Phelps, who collected his first Olympic gold on Saturday in the 400 individual medley, came through late in the race to take second place in 1:47.08.
Both men, however, were denied gold in the last race of Sunday night when South Africa scored a runaway win in the men's 4x100 freestyle relay.
Phelps and his U.S. team mates had to settle for bronze, while Thorpe's Australia were out of the medals.
All the focus in the 200 has been on Phelps and Thorpe but defending Olympic champion van den Hoogenband looked the most dangerous in the semi-finals, swinging through smoothly to clock the fastest overall time of 1:46.00.
He also produced the fastest relay split of the night to lift the Dutch to silver ahead of the U.S. in the relay.
The 26-year-old beat Thorpe into second place at the 2000 Games and although he has suffered consecutive beatings by the Australian at the 2001 and 2003 world championships he looks in the sort of form which proved so devastating in Sydney.
American world record holder Natalie Coughlin established herself as favourite for the women's 100 metres backstroke gold when she set an Olympic record in the semi-finals.
Seventeen-year-old Laure Manaudou of France, who won Sunday's women's 400 metres freestyle gold, was second-quickest in the backstroke semi-finals and will be fired up for a second shot at gold on Monday.
Leisel Jones, Olympic 100 breaststroke silver medallist in 2000, looked well placed to go one better when -- like Coughlin -- she set an Olympic record in Sunday's semi-finals.
Jones clocked 1:06.78, not far outside the world record of 1:06.37 she set in the semi-finals of last year's world championships, but she will need no reminding that records in semi-finals are no guarantee of gold because she had to settle for bronze in the ensuing final at the worlds.
World champion Aaron Peirsol signalled a strong bid for Olympic gold in the men's 100 backstroke final with the fastest semi-final time.
Defending Olympic champion Lenny Krayzelburg, Peirsol's American team mate, was second in the other semi-final behind Japan's Tomomi Morita.