Alderweireld - who has 24 caps for Belgium - is entering the final year of his contract at the Amsterdam Arena which has alerted teams such as Atletico, Liverpool, Everton, Tottenham and Spartak Moscow.
Norwich City agreed a fee for the centre-back in July, but a deal between the player and Premier League club could not be reached.
And Overmars confirmed that the Copa del Rey winner had also made a bid for the 24-year-old, but it had not come close to their valuation.
"We rejected the offer from Atletico de Madrid for Toby Alderweireld," he told De Telegraaf.
"We were contacted this weekend but it was not considered sufficient for a player of the national team of Belgium."
Alderweireld made 33 appearances for Ajax in the Eredivisie last season, and has played in all four matches so far this season.
Overmars also revealed he is still looking to bring players to the Amsterdam Arena before the end of the transfer window.
"I'm trying to negotiate with anyone and everyone," he added.