Blackwell said: "He's a player we have looked at before. I've had my eye on him for a year or two but we couldn't agree terms with Colchester.
"I'm delighted to finally get my man, although I was surprised Boro would let him go."
Dublin-born Yeates, who started out as a trainee at Tottenham where he had loan spells at various clubs, joined Colchester for an undisclosed fee in July 2007.
Former Boro manager Gareth Southgate signed Yeates in July last year for a reported fee of £750,000, but despite making 21 appearances this season he did not figure in new boss Gordon Strachan's plans.