Just read this thread. Here's what PokerStove says about the hand:
32,508 games 0.005 secs 6,501,600 games/sec
Board: 3s Js 9h
Dead:
equity (%) win (%) / tie (%)
Hand 1: 47.2499 % [ 00.47 00.00 ] {
}
Hand 2: 52.5655 % [ 00.53 00.00 ] { AJo }
Hand 3: 00.1846 % [ 00.00 00.00 ] { A6o }
So, top pair top kicker is a 52% favorite. Your three kings, flush outs, and runner-runner straight outs put you at 47%. The guy with ace-high (I used A6o here but it should be the same for any Ace-small combo) will only win this pot when hell freezes over. I think that's more of a chance than you need to justify the call, so you made the right play. Win some, lose some.