The 31-year-old joined Jonas Eidevall's side over the winter after running down her contract at Changchun Zhuoyue and has been an integral part of the team since.
Rafaelle has started all four of the Gunners' games this term alongside Leah Williamson in the heart of defence and scored her side's third goal in last weekend's 4-0 North London derby win over Tottenham Hotspur at the Emirates.
The Brazil international came off with a knock in the dying embers of that game, but she recovered in time to make the first XI for the second leg of their Champions League second-round qualifying tie with Ajax.
However, Rafaelle was only on the pitch for 38 minutes before picking up another injury, as Lotte Wubben-Moy replaced her for the remainder of that 1-0 victory.
Arsenal have now confirmed that the defender has sustained a metatarsal fracture in her foot, and she will be out for a number of weeks while she recovers.
Rafaelle will also not be available for Brazil during their upcoming clashes with Norway and Italy, and the former Palmeiras centre-back will most likely aim for a return in mid-November.
Rafaelle came through the college system at the University of Mississippi before spending time with Houston Dash, Sao Francisco BA, America Mineiro, Changchun Zhuoyue and Palmeiras.
The defender has already chalked up two strikes in eight appearances for Arsenal since her January arrival, as well as scoring eight goals from 75 appearances for the Brazil national team.
With Rafaelle sidelined, Arsenal held out for a 1-0 win over Ajax in Amsterdam thanks to Vivianne Miedema's strike, which sealed their place in the Champions League group stage after a 2-2 draw in the first leg at home.
Speaking to arsenal.com earlier this summer, Rafaelle opened up on her dream to represent the North London club in Europe, saying: "A big part was the club's history, like playing in the Champions League and big tournaments, and the Women's Super League itself is really strong.
"I was looking for a strong league. After being in China it felt like I was hiding from the world, so I wanted to be in a league where I could show people my football. I also wanted to be in a country where I could have some independence because in China I couldn't speak the language at all.
"I also had offers from French and Spanish clubs, but I wouldn't be able to immediately speak the language and live my own life. So everything together - Arsenal's history, my own independence and the level of the league - was really good for me."
Arsenal also lost Beth Mead to a nasty clash of heads with Lisa Doorn against Ajax, but the Gunners shared a reassuring update on her condition after the game, posting a picture of the England forward on the plane home with the caption: "Don't worry Meado's all OK! Thanks for your concern and love, Gooners."
However, Mead's withdrawal led to confusion on the bench after Eidevall was under the impression that he could make a substitution, but UEFA have since confirmed that concussion substitutes are not permitted in the Women's Champions League.