The match appeared to be heading for extra-time in the tense closing moments when Eddie Barrett broke through the Newmarket defence and passed the ball to Paudie Nevin.
He found Keane and the corner-forward buried his shot into the net from close range.
Clare champions Newmarket, who had Tipperary's All-Ireland-winning manager Liam Sheedy acting as a special advisor, will feel that this was one they left behind, considering they shot five consecutive second-half wides in a period of dominance.
However, on the other hand, De La Salle were also off target on nine occasions before the break, going in 0-8 to 0-7 ahead at the whistle.
Bryan Phelan opened the scoring for the Waterford City team inside a minute with a long-range pointed free but in a dogged first half they couldn't exert their dominance on the scoreboard, mainly due to their wayward shooting up front.
Phelan added another point before the break to bookend some good scores by Keane (2), John Mullane, Paudie Nevin and mid-fielder Dean Twomey.
Newmarket began the second period brightly, showing that they meant business by taking the lead temporarily through a pair of points by Shane O'Brien Snr.
A Jake Dillon free, and a Mullane effort from play, regained the advantage for the visitors by the 41st minute and then a Mike McInerney score for the hosts had the teams level again, at nine apiece, a minute later.
That leveller was then followed by a vital score by De La Salle's Twomey as Newmarket fought back admirably to try and snatch a first Munster club win in over 30 years.
McInerney made it 0-10 all with five minutes remaining after his thunderbolt shot earlier in the half hit the crossbar to let the Deise side off the hook.
However, the Waterford men had the decisive last act when Keane was in the right place to fire home the winning goal and set up another Munster final contest with Tipperary champions Thurles Sarsfields.
Scorers -- De La Salle: J Keane 1-2, D Twomey, J Mullane, B Phelan (2f) 0-2 each, J Dillon (f), P Nevin 0-1 each.
Newmarket-on-Fergus: C Ryan 0-4 (2f, 1 '65), M McInerney, S O'Brien Snr 0-2 each,D Barrett, S O'Brien Jnr 0-1 each.
De La Salle -- S Brenner; C Watt, I Flynn, S Daniels; E Madigan, K Moran (capt),B Phelan; E Barrett, D Twomey; P Nevin, D Greene, J Dillon; J Keane, J Kennedy,J Mullane. Subs: O Keevers for Watt (36), C Sheehan for Madigan (49), S McNulty for Greene (50).
Newmarket-on-Fergus -- D Duggan; S O'Connor, J McInerney, E O'Brien; N O'Connor, E Barrett (capt), A Barrett; E Hayes, M O'Hanlon; D Barrett, C Ryan, M McInerney; S O'Brien Jnr, A Kilmartin, S O'Brien Snr. Subs: J Liddy for Kilmartin (38), S Kelliher for S O'Brien Jnr. (50).
Ref -- J Ryan (Tipperary)