Marta picked up the Women's Player prize at the FIFA Best Awards, while Lyon's triumph in the Women's Champions League was also recognised.
Reflecting Real Madrid's dominance in the men's equivalent, Lyon - 16 times French champions - stormed to their third straight Champions League win, becoming the first women's team to do so.
But it was Brazil star Marta, often regarded as the best female player of all time having scored 15 World Cup goals, who edged out Lyon duo Ada Hegerberg - who registered a record 15 goals in the successful Champions League campaign - and Dzsenifer Marozsan to the award.
Marta scored 13 NWSL goals in 2017 and contributed four more in 17 appearances for the Orlando Pride in 2018.
The Brazilian is a five-time FIFA World Player of the Year and was a runner-up for Best Women's Player in 2016 before being left out of the final three one year later
Congratulations, Marta
— FIFA Women's World Cup (@FIFAWWC) September 24, 2018
Winner of #TheBest FIFA Women's Player 2018 #FIFAFootballAwards pic.twitter.com/aCxCn2TIFy
Lyon's triumph was recognised in the Best Women's Coach award section, however.
Reynald Pedros - a former France international - saw off competition from Japan's Asako Takakura and Sarina Wiegman of the Netherlands.
Pedros, who took charge of Lyon in 2017, succeeded Gerard Precheur at Lyon after the fellow Frenchman finished third behind Nils Nielsen and winner Sarina Wiegman in 2017.