technically no. But next season they're going house shopping together and of course they ARE having a kid together so they'll be together by next season.
Actually they are together. I hate to ruin season 6 for you (or any season of Bones) but since you asked...
When Vincent was killed by Jacob Broadsky in the second to last episode, Brennan stayed at Booth's apartment so he could protect her. In the middle of the night she went to Booth because she was having a hard time dealing with it all and felt guilty about the way in which he died and what he said to (what she thought to be) her. So he counseled her and they fall back onto the bed as she's crying in his arms. Brennan then tells Angela that "she got into bed with Booth last night" and Angela asks what happened exactly after she got into bed with him and as she's about to answer Hodgins interrupts and we never get to hear the end of the conversation. At the end of the episode Brennan links arms with Booth and he smiles and they turn and walk away (so you know something happened). In the finale there are many comments about how B&B are acting odd (mostly by Max) and some comments about if B&B ever had a baby.
Then after Angela gives birth to her and Hodgins' son, Brennan and Booth are walking down the street and she tells him that she's pregnant and he's the father.
The writers have announced that B&B did sleep together that night, are indeed a real couple now and are expecting a baby! It's also left to interpretation whether or not they slept together more than once between the second to last episode and the finale.
Short answer: YES THEY ARE TOGETHER AND THEY ARE EXPECTING A BABY.
