Stoughton wasn't the only veteran to fall in the first draw of the eight-team men's field.
Ontario's Glenn Howard and his team from Penetanguishene, Ont., lost 8-6 to John Morris of Vernon, B.C.
Reigning Olympic champion Kevin Martin had a duel against Winnipeg's Mike McEwen, but the Edmonton skip finished with a 5-3 victory.
Toronto's John Epping was also victorious when he got by Calgary's Kevin Koe 9-8.
Jacobs and his foursome from Sault Ste. Marie led from the beginning and widened the gap 4-1 after a double takeout in the fifth end scored two.
Even though the two-time world and three-time Brier champion Stoughton is beloved by local fans, the knowledgeable crowd of 10,214 at MTS Centre cheered in appreciation of Jacobs' tough shot.
Stoughton bounced back with a pair in the sixth end to make it 4-3, but Jacobs stretched the lead to 6-3 with a draw that gave him a pair in the eighth.
Stoughton added one with the hammer in the ninth to make it 6-4.
Jacobs, 28, was a runner-up at this year's world championships.
Stoughton, 50, is playing in his fifth Trials and has said this is his last crack at trying to earn an elusive berth to an Olympic Games.