Alfred made her usual slick start and remained clear in heavy rain on a sodden track to come home in a national record 10.72 seconds.
World champion and race favourite Sha'Carri Richardson took silver in 10.87 but the American never really threatened and her compatriot Melissa Jefferson claimed bronze in 10.92.
Double Olympic champion Fraser-Pryce, appearing in her fifth Olympics, was listed as 'Did Not Start' shortly before the semi-finals and her lane remained empty.
Social media footage later emerged of her and Jamaican team members arguing with officials who appeared to be refusing to let her in.
Fraser-Pryce was heard saying: "They've changed the rules, we always come through this gate."
World Athletics said it was still awaiting for official confirmation of the reason for her absence from the Jamaican team.
With Fraser-Pryce missing the heat, Richardson was slow out of the blocks and could not overhaul Alfred.
It was almost a repeat of last year’s world championships when Richardson sneaked into the final as a fast loser and won the title from lane nine.
There was to be no repeat this time, however, as Alfred hit her stride brilliantly and splashed home for a glorious gold.
The United States' 28-year gold medal drought in the event goes on. Gail Devers was their last winner in 1996. Marion Jones was stripped of her 2000 Olympic gold for doping.
It also ended Jamaica’s stranglehold on the event after they won the last four Olympic golds and 10 of the 12 available medals.