Fowler and veteran defender Aivi Luik suffered mild concussions in separate incidents at Tuesday's closed training and were subsequently scratched from Thursday night's game at Suncorp Stadium.
Caitlin Foord is now the only recognised striker available against the African side, with Kerr (calf), Kyah Simon (knee) and Fowler all sidelined.
The 20-year-old had replaced Kerr as Foord's starting strike partner in the 1-0 win over Ireland.
Fowler's concussion and Kerr's injury will only increase scrutiny on the gamble to carry Simon through the tournament's early stages, with a view to using her off the bench as an impact substitute later.
Simon was the shock inclusion in the squad announced on July 3, having not played a game since rupturing her left anterior cruciate ligament in October.
Football Australia said Fowler and Luik, who wasn't used against the Irish, were fully recovered and in return-to-play protocols.
FA's concussion protocol rules players out for at least six days, which opens the door for Fowler and Luik to play in the final group game against Canada in Melbourne on July 31, provided they clear the return-to-play program.
Fowler was walking laps at training on Wednesday then started running later in the 15-minute window available to media.
Kerr will be reassessed after the Nigeria game but given the tight, four-day turnaround to the Canada clash she appears unlikely to play and there is currently no timeline on her return.
The striker and her teammates have insisted Kerr will return to action during the tournament.
A week on from suffering the calf strain that has the nation holding its breath, Australia's superstar captain was walking laps on Wednesday, the most activity she has carried out in public since the injury was announced.
Simon was also walking laps at Brisbane's Perry Park on Wednesday but Luik was not.
With coach Tony Gustavsson unlikely to change the successful midfield pairing of Kyra Cooney-Cross and Katrina Gorry, veteran playmaker Emily van Egmond appears the likely option to play alongside Foord.
Tameka Yallop, who has recovered from a corked thigh, and dynamo Alex Chidiac are other options to come in, while Cortnee Vine and Hayley Raso are the first-choice wingers.
Defender Alanna Kennedy was back in main training after missing Sunday and Monday for loading reasons.
As the only team in Group B with three points from their opening game, Australia can seal progression to the knockout stages with victory over Nigeria, who have one point so far.
If Canada (one point) and Ireland (zero) draw in Perth on Wednesday night, a win on Thursday would lock in top spot for the Matildas ahead of their third group game.
