Rooney was heavily linked with the Blues, with Jose Mourinho having at least two bids turned down for the 27-year-old and only ending his interest a week before the transfer window closed.
Since then, Rooney has become only the fourth United player to reach 200 goals for the club and has spoken warmly about the reception he has received from supporters and his hope he would get the chance to score many more.
Although he is still to pledge his future to United, it was taken as the most positive sign yet Rooney would be happy to stay if successful negotiations can be concluded on an extension to a contract that expires in 2015.
But Gill, now a United director after standing down from his post to take up a role on UEFA's executive committee, has revealed the Chelsea option was a non-starter anyway.
"We are not in the business of strengthening our key competitors in England," Gill told BBC Radio Five Live's Sportsweek programme.
"You have to see our response when Gabriel Heinze wanted to join Liverpool (in 2007).
"We went to a Premier League arbitration panel to show that we didn't commit to him moving within England for a certain sum of money.
"We wanted to keep (Rooney) in any event and not sell him overseas.
"You don't win football matches with money in the bank.
"You want players on the pitch. Wayne Rooney has been, and will continue to be I am sure, a great player for Manchester United."
The situation is slightly complicated in the sense Rooney could buy himself out of the remaining year of his contract at the end of the season and pursue an apparent desire to work under Mourinho.
Much is likely to hinge on discussions between United and Rooney's camp about an extension to the estimated £250,000-a-week deal he signed after his previous stand-off in 2010.
It has been suggested in the past United may demand a reduction in those terms, which would be unacceptable to the England frontman.
Gill is slightly detached from such proceedings now but he does feels talks are bound to start at some point.
"Yes, I am sure they will look at it," said Gill.
"We have an approach to dealing with players' contracts at Manchester United that has stood us in good stead for many years.
"I am sure (executive vice-chairman) Ed (Woodward), (manager) David (Moyes) and the owners will continue with that policy."