That was 2:04, "Dead Drop," the episode in which Sydney tracks down the operational bible and Jack feels compelled to set Irina up.
Frankly, though, I can't think of a time that they hugged before that. In fact, last season when Jack reached out to pat Sydney on the shoulder (for choosing to stay with SD-6 and not risk her life by departing at the end of "The Box"), it was an extremely awkward moment because of their long estrangement. Part of what made the moment in "Dead Drop" so compelling was that it was a kind of revelation--the first gesture of that kind between father and daughter since perhaps Sydney's early childhood.
If you can think of other times when they've actually hugged, please let me know the specifics.
