The club revealed the 'Story Of My Life' singer was behind the design on Monday after the poll had closed.
In the wake of the announcement some fans have criticised the club and questioned the credibility of the vote.
Doncaster Rovers say the voting process "was all was fair and above board".
Writing on Twitter one fan said: "I wonder if the vote was rigged or that shirt actually won??? #drfc."
The design for the 2016/17 away kit submitted by Tomlinson and his grandfather was one of five put to the public vote. It received 33.7% of votes while the second placed design polled 26.2% of votes.
After being announced as the winner Tomlinson told the club's website: "I designed the kit with my granddad when I was home a few weeks ago.
"We used to go to Belle Vue together so it has always been a family affair with us and to now have a hand in next seasons away shirt is brilliant. I can't wait to see my team wearing it".
Doncaster Rovers revealed the winning design in February, but did not say who was responsible.
At the time it said the winner would be taken to Thailand to see the first stage of manufacturing.
Fans have also raised their eyebrows at the clubs decision to give away 20 shirts signed by Tomlinson to fans who pre-order the strip.
One asked if he could receive a signed version of the new home strip, also chosen from a poll of fan designs.
Other fans however, have tweeted their support for Tomlinson's design.
A spokesperson for Doncaster Rovers said: "The process for receiving kit designs, shortlisting and the public voting for our kit design competition followed strict legal guidance to ensure that the club adhered to competition law and that all processes were fair.
"We are aware that the result of the competition has attracted some negative feedback, but we can assure our fans that the voting process for the 2016/17 shirt designs was all was fair and above board."
Tomlinson, who was part of a failed bid to buy Doncaster Rovers in 2014 , signed for the club as a non-contract player in August 2013 and made his debut for the side's reserve team in February 2014.

The popular Smart Sheriff app has vulnerabilities that could leak children's personal details or allow the phone to be hacked, the study says.
The app's developer says it has since addressed some of the issues raised in the report, although this has not been independently verified.
South Korea mandated in April that all children's phones must be monitored.
Anyone under 19 who buys a smartphone must install an app that can filter and block harmful content.
The University of Toronto report is based on two separate security audits, one conducted by researchers at the Citizen Lab with the university's Munk School of Global Affairs, and the other by auditing firm Cure53.
Smart Sheriff was developed by a consortium of telecommunications companies known as the Korean Mobile Internet Business Association (Moiba). It has been downloaded by hundreds of thousands of users in South Korea.
The app allows parents to control the apps on their child's mobile phone, as well as schedule when the phone can be used. It can also alert parents when it detects trigger words such as "kill", "rape", and "suicide", according to earlier news reports.
However, the new report found that children's personal details and browsing activity were not secure on the app, parental limits could be easily disabled and Smart Sheriff's design and infrastructure were insufficiently protected.
The report said this could "allow children to bypass parental protections, allow malicious attackers to disrupt access to every user's device, and interfere with the operations of the service".
"This case shows precisely how good intentions can end up seriously wrong â€” in this case, a government-promoted parental monitoring application actually putting children at greater, rather than less, risk of harm," said Citizen Lab's director Ron Deibert.
News agency AP quoted independent researcher Collin Anderson, who worked with Citizen Lab on the report, as saying: "Smart Sheriff is the kind of baby sitter that leaves the doors unlocked and throws a party where everyone is invited."
Citizen Lab said it had informed Moiba of the vulnerabilities. Moiba has since released updates, the latest on 25 August, to fix the issues raised. However, researchers said they had yet to independently verify if all vulnerabilities had been addressed.
The BBC's calls to Moiba on Monday were not answered.
The introduction of the child monitoring law in April sparked some controversy, with critics raising privacy concerns.
Doncaster Rovers fans have reacted angrily to One Direction star Louis Tomlinson and his grandfather winning a competition to design the football club's new away kit.
[NEXT_CONCEPT]
A child monitoring phone app funded by the South Korean government has major security flaws, a new report says.