After Vincent is shot Booth insists that Brennan stay the night at his apartment for her safety. Shaken up she goes to his bedroom in the middle of the night and ends up crawling into 床, 床上 with him.
There is no visual evidence of sex so it's not really confirmed until the pregnancy announcement which is in season 6 episode 23: 'The Change in the Game', but it's implied when she confides in Angela the 下一个 day.
