Paula Dapena, from third division club Viajes InterRias FF, turned her back and sat on the pitch before a friendly against Deportivo La Coruna as both teams paid tribute to the late midfielder.
Maradona, 60, died of a heart attack on International Day for the Elimination of Violence against Women, 25 November.
"As soon as I found out that there would be an act in his memory I refused to observe the minute's silence for a rapist … and abuser," Ms Dapena told Spanish media outlet AS.
The 24-year-old school teacher said it would be "hypocritical" for her to ignore Maradona's past and observe a minute's silence after not observing the same tribute for victims of violence against women.
While teams commemorated International Day for the Elimination of Violence against Women, they did not hold the same minute's silence as was done for Maradona.
"It [Maradona's death] totally overshadowed that day," Ms Dapena said. "We went from putting the spotlight on the death of women due to this cause to talking only about Maradona and what an idol he was for everyone."
She added: "For me, from a football standpoint, Maradona had spectacular skills and qualities. But as a person, he left a lot to be desired."
In 2014, Maradona denied accusations of domestic violence after a video circulated purporting to show him strike wife Olivia.
"I grabbed the phone but I swear to God that I have never hit a woman. The incident was over immediately. I threw the phone but nothing else," he said in 2014.
Ms Dapena said she was surprised to be the only female footballer that refused to honour Maradona, and by the harassment she has received since.
"It's not just me that has been harassed on social media but also my teammates," she said.
"We have also received death threats and messages such as 'I'm going to find your home address and go there and break your legs.'"