Disgruntled supporters of both teams organised the fans' match to clash with the Rovers' Checkatrade Trophy tie against the Mariners, which ended 1-1 before Doncaster claimed victory in a penalty-shoot out.
Just 862 fans watched the encounter at Blundell Park - with a total of 1,074 watching the supporters' match played at the same time - beating the official attendance by more than 200.
The boycott game ended 1-0 to the Rovers side, with fan Dave McDonald scoring the winning goal.
Rovers' supporters' spokesman Louis Bailey said: "With an attendance of 161 at the game and 913 watching online, we had a total of 1074 people watching our game.
"In addition we've raised Â£1200 and counting for local charities, so all in all we're very pleased."
He added: "In terms of the relative facilities and 'pulling power' for us to have that many people attending and watching is massive. We've also raised a good chunk of money and got a large group of fans of backing us. Some from other clubs have donated already."
Grimsby's IMFC took on Rovers' Donny R'Sonists in the game to raise awareness of fans' anger at the competition which has been derided by football supporters across the country.
The competition sees Football League clubs playing against each other as well as U21 sides from Championship and Premier League teams but has been hit by low attendances, fan boycotts and protests over its format.
A spokesman for IMFC said: "The Checkatrade Trophy is a competition that many football fans disagree with and has united us regardless of who we support.
"We want to uphold the values and history of traditional clubs in England and Wales, without this competition being used as a backdoor to B league proposals."
"This was a great opportunity for us to raise awareness of our thoughts on this competition, whilst also generating money for three excellent charities."
Money will be split between Grimsby Town Disabled Supporters Club, Inspire TCI and Bluebell Wood Children's Hospice.