Defending champion Craig Stadler (67), Morris Hatalsky (67) and second-round co-leader Gil Morgan (69) shared second place at 12-under-par 204.
Irwin had a very up-and-down front side on Sunday as he shared the overnight lead with Morgan, but played the first 11 holes in even-par. Morgan cruised into the lead as he made it around the same span of holes in 3 under par.
Irwin's fortune changed at the par-3 12th. He drained a 45-foot birdie putt from the other side of the green to get to 10 under par for the championship. He made it two in a row with a 6-footer to reach 11 under par and trail Morgan and Stadler by a single stroke.
The par-5 14th knocked out both Morgan and Stadler. Stadler, a few groups ahead of Irwin and Morgan, knocked his third on the putting surface, but the ball spun back into the fairway. His pitch stopped 12 feet from the stick and he missed the putt to fall out of first.
Stadler wasted little time in getting back into the lead. He rolled in a 35-foot birdie putt at the 15th to get back to 12-under and soon the top spot would be his alone.
Morgan hit almost the same third shot into 14 and left with the same result, a bogey. Morgan would not make another birdie the rest of the way and fell down the board.
Irwin's approach at the 15th stopped 10 feet from the hole. He poured that birdie putt in and was now tied for the lead at 12 under par.
Hatalsky joined the lead with a short birdie putt at 16, but he and Stadler had to scramble to save pars at 17. Both found the bunker short of the green at 17, but both got up and down.
Irwin got a tad lucky on the par-3 17th. His ball hit the hill guarding the flagstick and slowed it down. The ball stopped 10 feet past the cup and he rolled it in for a birdie and the lead at minus-13.
Both Stadler and Hatalsky laid up short of the green with their second shots at Pebble Beach's famous par-5 closing hole. Neither left themselves with good birdie tries as Hatalsky two-putted from the top of the green 35 feet away and Stadler missed from 30 feet.
They waited to see if Irwin would slip up on his way into the clubhouse. His drive went a little right at 18 and he laid up to 149 yards. Irwin knocked his approach 25 feet left of the hole and he two-putted for his third win of the 2005 season and 43rd on the Champions Tour, extending his record further.
Mark McNulty fired a 7-under 65 on Sunday to finish alone in eighth at minus-10.
Jay Haas shot a 3-under 69 in the final round and Lonnie Nielsen managed a 1-under 71 to share ninth place at 8-under-par 206.