Wells (2-3) logged his first win since April 4, a span of 10 starts, handcuffing the Astros on one run, surrendering a pair of walks while striking out four.
Jeff Samardzija, James Russell and Sean Marshall combined for two innings of shutout ball and Carlos Marmol threw a scoreless ninth for the Cubs, who clinched their three-game series at Wrigley Field.
Soto launched a solo homer in the fifth, giving Chicago a 2-0 lead, and added an RBI single in the eighth.
Marlon Byrd also contributed a bases-empty shot among his two hits for the Cubs.
Houston's Wandy Rodriguez (6-7) pitched well in the loss, yielding two runs on three hits over seven innings.
Carlos Lee went 3-for-4 with an RBI single for the Astros.