It is the first time Johnson has used powers that allow him to call in applications with strategic importance for the whole city. He cited Columbus Tower's contribution to Crossrail as one of the reasons for his decision.
London Assembly member Jenny Jones said: "The mayor said he would leave these decisions to boroughs, but with Crossrail money at stake he overruled Tower Hamlets. If he has changed his mind about respecting local democracy he needs to make his criteria clear."
A London Councils spokeswoman said: "Boroughs are best placed to make decisions as they understand the needs of their local area."
GVA Grimley advised developer Commercial Estates Group on its bid. Planning director Julian Carter said: "It is reassuring that the mayor will use his powers to take over applications that are strategically important."