It was the ex-Everton midfielder's first in 28 Wigan appearances and put the Latics in front for the third time.
But they had to be content with a share of the points in their fight for Premiership survival after Robbie Keane made it three apiece.
Wigan had skipper Arjan de Zeeuw back to make his 200th appearance and Henri Camara got his first start since December.
Spurs, anxious to bounce back from their European disappointment, had Pascal Chimbonda returning to the JJB for the first time since his acrimonious departure.
There was a sensational start with both sides grabbing a goal inside the opening four minutes.
Ironically, Chimbonda's first touch saw him penalised for a foul on Emile Heskey and, from Denny Landzaat's free-kick, Heskey headed in his third in as many games.
Spurs came up with an instant reply with Keane threading a terrific ball through for Dimitar Berbatov who poked a right-foot shot beyond John Filan.
Spurs almost had a second when the Bulgarian beat the offside trap to set up a shot for Keane, but Landzaat did well to block it.
The Latics were back in front after 30 minutes thanks to a sensational strike from Leighton Baines.
The England Under-21 left-back latched on to a headed clearance and let fly with an unstoppable volley from the edge of the area which flew past Paul Robinson.
This time the lead last five minutes as Spurs grabbed a controversial equaliser from the penalty spot through Keane .
Jermaine Jenas was pushed by Baines outside the box and went down as Filan raced out to meet him and Keane made no mistake as he wrong-footed the keeper from the spot.
Wigan should have been in front at half-time after Robinson beat out a Paul Scharner header and Kilbane put the follow up over the bar.
The Latics did lead again when Kilbane headed in from Ryan Taylor's corner, but Spurs salvaged a point when Keane lobbed Filan from 25 yards after spotting him off his line.