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The Doctor used a device called The Moment to destroy Daleks and Time Lords alike. (previous timeline)

In fact, the Doctor - with the help of 12 of his other incarnations - froze Gallifrey inside a pocket universe (in "The Day of the Doctor"). Due to the laws of time, however, the so-called "War Doctor" was unable to remember interacting with his future selves, and (because he didn't remember it) when he regenerated into the Ninth Doctor he believed - as did the universe - that the Time Lords had been destroyed. It was not until his Eleventh incarnation, when he was able to finally retain the memories of the event, that the Doctor realized that the Time Lords actually survived. (current timeline)