Running his second race since setting a new world mark of 9.78 last September, Montgomery almost turned his ankle over after 75 metres but hung on, dipping first at the tape to snatch a morale-boosting victory by just 0.01 seconds.
Johnson set an Australian record of 9.93, the fastest time in the world this year, in Mito, Japan on Monday and put a positive spin on his narrow defeat in Osaka.
For Montgomery, beaten into second place by Canadian Nicholas Macrozonaris in Mexico City last weekend, victory gave him a welcome boost before the start of the European season and the world championships in Paris this August.
Japanese 200 metres specialist Shingo Suetsugu finished third behind Montgomery and Johnson in 10.16 with American Bernard Williams fourth in 10.17.
Meanwhile, world indoor champion Tyree Washington won the 400 metres in 44.97 with fellow American Calvin Harrison second in 45.32. Australian Clinton Hill took third in 45.39.
Dudley Dorival of Haiti won the 110 metres hurdles in 13.49 ahead of Jamaican Maurice Wignall (13.50) and American Duane Ross (13.51) at the Nagai Stadium in Osaka, venue for the 2007 world championships.
American Mark Crear, who won at the season-opening grand prix in Brazil last weekend, clocked 13.58 to finish fourth after getting off to a poor start from lane four.
Results...
100 metres: 1. Tim Montgomery (U.S.) 10.04 seconds 2. Patrick Johnson (Australia) 10.05 3. Shingo Suetsugu (Japan) 10.16
400 metres 1. Tyree Washington (U.S.) 44.97 2. Calvin Harrison (U.S.) 45.32 3. Clinton Hill (Australia) 45.39
5,000 metres 1. Abraham Chebii (Kenya) 13:21.45 2. Luke Kipkosgei (Kenya) 13:23.38 3. Gebreegziabher Gebremariam (Ethiopia) 13:23.57
110 metres hurdles 1. Dudley Dorival (Haiti) 13.49 2. Maurice Wignall (Jamaica) 13.50 3. Duane Ross (U.S.) 13.51
400 metres hurdles 1. Eric Thomas (U.S.) 49.06 2. Kemel Thompson (Jamaica) 49.24 3. Dai Tamesue (Japan) 49.60
Triple jump 1. Kenta Bell (U.S.) 17.01 metres 2. Jadel Gregorio (Brazil) 16.83 3. LeVar Anderson (U.S.) 16.63
Pole vault 1. Nick Hysong (U.S.) 5.50 2. Satoru Yasuda (Japan) 5.50 3. Daichi Sawano (Japan) 5.50
Hammer 1 . Koji Murofushi (Japan) 82.95 2. Adrian Annus (Hungary) 79.74 3. Andrey Skvaruk (Ukraine) 79.29
4 x 100 metres relay 1. Japan A 38.56 2. United States 38.75 3. Japan B 39.15
4 x 400 metres relay 1. Japan A 3:02.97 2. Japan B 3:03.60 3. Australia 3:05.72
100 metres 1. Chrystie Gaines (U.S.) 11.03 2. Kelli White (U.S.) 11.07 3. Mary Onyali-Omagbemi (Nigeria) 11.32
1,500 metres 1. Judit Varga (Hungary) 4:12.49 2. Margaret Ngotho (Kenya) 4:13.64 3. Lucy Wangui (Kenya) 4:13.87
5,000 metres 1. Leah Malot (Kenya) 15:32.45 2. Jane Wanjiku (Kenya) 15:32.62 3. Kazue Ogoshi (Japan) 15:33.85
400 metres hurdles 1. Yvonne Harrison (Puerto Rico) 55.63 2. Brenda Taylor (U.S.) 55.65 3. Sandra Glover (U.S.) 55.68
Long jump 1. Bronwyn Thompson (Australia) 6.65 2. Grace Upshaw (U.S.) 6.61 3. Maho Hanaoka (Japan) 6.54
Hammer 1. Olga Kuzenkova (Russia) 71.33 2. Brooke Krueger (Australia) 67.40 3. Bronwyn Eagles (Australia) 67.10
Shot put 1. Valerie Adams (New Zealand) 18.93 2. Krystyna Zabawska (Poland) 18.41 3. Lee Myung-sun (South Korea) 17.41
High jump 1. Elena Slesarenko (Russia) 1.92 2. Miyuki Aoyama (Japan) 1.89 3. Petrina Price (Australia) 1.89
4 x 100 metres relay 1. International Selection 43.77 2. Thailand 44.49 3. Japan A 44.69—Reuters