Tomlinson, who hails from Doncaster, entered the competition on the club's website and his all-black design topped a public poll with 33.7 percent of votes.
The singer reacted on Twitter by writing: "Soooooo me and my Grandad Len won the competition of designing the new Donny away shirt. Pretty sick."
But supporters claimed a fix, with Twitter user Jake Laughton complaining: "You kidding me, the away shirt was coincidently designed by Louis Tomlinson and it coincidently won?! Awful, just awful!!!!!"
Thomas Bailey tweeted: "Lad from One Direction wins a competition to design the Doncaster away kit. Definitely not an attempt at improving shirt sales..."
But a spokesman for third-tier 'Donny' said that while feedback had been "mixed", the voting process had been "fair and above board".
Tomlinson, 24, made a much-publicised appearance for Doncaster's reserve team two years ago, generating a crowd of over 5,000.
Part of his prize for winning the shirt competition will see him travel to Thailand to see his design being made.