The One Direction singer was announced as the new boss of Doncaster Rovers last month, after his joint offer with former club chairman John Ryan was officially accepted by shareholders.
They established The Tomlinson/Ryan Trust to support and develop the team after the Rovers were relegated to the third tier of football in May.
They launched a money-raising campaign on Crowdfunder to help them hit their £2 million target. Tomlinson and Ryan also agreed to donate a six-figure sum themselves.
The pair was dealt a blow on Thursday after Football League officials, who still had to approve the bid, rejected the duo's takeover attempt amid concerns the two business partners do not have the proper finances to run the club properly.
The news emerged on the same day their crowdfunding campaign closed, £1.24 million short of their goal.
Breaking the news to fans on Twitter, Tomlinson writes: "I'm absolutely gutted the Doncaster Rovers deal is not going ahead. I am desperate for the club to be given the recognition it deserves.
"I was explicitly told that the deal to buy the club was not dependent on the money raised by Crowdfunding. Unfortunately I was misled.
"My passion for Doncaster Rovers remains as strong as ever, and I hope that I can still be involved with the club moving forward! And to all the Doncaster Rovers fans, I will do all in my power to help the club succeed. I really do love the club!"