Alker claimed the $1.7m prize for finishing top of the tour's points list for the second year running, but he missed replicating his win last year in the final tournament - Charles Schwab Cup Championship - falling just short on a dramatic final hole, leaving 67-year-old German Bernhard Langer as the tournament winner.
Alker earned $460,000 for finishing tied for second with Australian Richard Green, at 17-under, one shot behind Langer.
Alker, Langer and Green were level at 17-under when Alker and Langer teed off at the 18th hole, with Green in the clubhouse after his round.
Both had untidy approach shots, but Langer nailed a 30-foot (9.1m) putt and Alker came just a few inches short with his putt that would have sent them to a playoff.
It was Langer's 47th victory in 18 years on the Champions Tour.
He had a one-stroke lead over Alker heading into the final round, after shooting his age with a four-under 67 in the third round.
He led until bogeying the 17th hole, and while his shot-making on the final hole was patchy, he scrambled well enough before sinking a brilliant clincher.
"It still has to sink in," Langer told Sky Sport.
An emotional Alker paid tribute to his support team in earning him a second Charles Schwab Cup.
"This doesn't happen with just me … it's been a heck of a ride."
Alker was just one of seven players to have won the overall season title more than once.
"It means a lot. It's a season-long race, so consistency [is key] and you want to get some wins in there as well, and I am proud of the fact that I have kept that consistency over the last few years.
"Just competing with everybody out here on the Champions Tour has made me a better player, and I am very grateful for that."
