Merritt finished well clear of Santos, who was 0.56 seconds behind, and Pavel Maslak of the Czech Republic in third place.
"I still feel like I'm in top form," Merritt said after his first big race since the world championships in Moscow.
World Champion Svetlana Shkolina of Russia has won the women's high jump at 1.98m, beating countrywomen Anna Chicherova and Mariya Kuchina into second and third.
Results from the 12th round of the Diamond League series in Stockholm:
Men:
110m hurdles:
1. David Oliver (USA) 13.21
2. Sergey Shubenkov (RUS) 13.35
3. William Sharman (GBR) 13.36
200m:
1. Serhiy Smelik (UKR) 20.54
2. Jaysuma Saidy Ndure (NOR) 20.58
3. Rasheed Dwyer (JAM) 20.64
400m:
1. LaShawn Merritt (USA) 44.69
2. Luguelin Santos (DOM) 45.25
3. Pavel Maslak (CZE) 45.33
1500m:
1. Ayanleh Souleiman (DJI) 3:33.59
2. Silas Kiplagat (KEN) 3:33.92
3. Nixon Kiplimo Chepseba (KEN) 3:34.05
3000m steeplechase:
1. Hillary Kipsang Yego (KEN) 8:09.81
2. Gilbert Kirui (KEN) 8:11.55
3. Conseslus Kipruto (KEN) 8:12.35
Long jump:
1. Aleksandr Menkov (RUS) 8.18
2. Godfrey Khotso Mokoena (RSA) 8.06
3. Eusebio Caceres (ESP) 8.00
Discus:
1. Piotr Malachovski (POL) 65.86
2. Ehsan Adadi (IRI) 63.64
3. Martin Wierig (GER) 63.20
Women:
100m:
1. Kerron Stewart (JAM) 11.24
2. Alexandria Anderson (USA) 11.25
3. Barbara Pierre (USA) 11.29
400m hurdles:
1. Zuzana Hejnova (CZE) 53.70
2. Kaliese Spencer (JAM) 54.88
3. Dalila Muhammad (USA) 55.74
800m:
1. Eunice Sum (KEN) 1:58.84
2. Alysia Montao (USA) 1:58.96
3. Malika Akkaoui (MAR) 1:59.74
3000m:
1. Meseret Defar (ETH) 8:30.29
2. Mercy Chenoro (KEN) 8:31.23
3. Sifan Hassan (ETH) 8:32.53
High jump:
1. Svetlana Shkolina (RUS) 1.98
2. Anna Chicherova (RUS) 1.98
3. Mariya Kuchina (RUS) 1.94
Pole vault:
1. Silke Spiegelburg (GER) 4.69
2. Yarisley Silva (CUB) 4.59
3. Fabiana Murer (BRA) 4.59
Triple jump:
1. Caterine Ibargen (COL) 14.61
2. Olha Saladukha (UKR) 14.07
3. Hanna Knyazheva (ISR) 13.95
Shot put:
1. Valerie Adams (NZL) 20.30
2. Christina Schwanitz (GER) 19.26
3. Michelle Carter (USA) 18.56