The Brazil international, a €160million signing from Liverpool last month, came off the bench to break the deadlock before Ivan Rakitic sealed the win and kept the Catalans' hopes of a treble alive.
Coutinho was perhaps surprisingly left out of the starting line-up in favour of Andre Gomes at Mestalla as head coach Ernesto Valverde named a strong side that included Gerard Pique, who recovered in time from a knee problem.
Valencia had lost their last three matches in a row but looked the more dangerous in the first half, with Rodrigo Moreno powering their best chance off the underside of the crossbar.
Coutinho's half-time introduction changed the course of the game, though, the midfielder sweeping home a cross from fellow former Liverpool man Luis Suarez, who also set up his first goal for the Premier League club back in February 2013.
Rakitic finished in style after more good work from Suarez, meaning Barca will meet Sevilla in the final in a repeat of the 2016 showdown, after Vincenzo Montella's side beat Leganes 3-1 over two legs.
Both goalkeepers were tested in the opening 10 minutes, with Jasper Cillessen claiming a Francis Coquelin shot before Lionel Messi's free-kick was beaten acrobatically away by Jaume Domenech.
The end-to-end nature of the game continued as Rodrigo rattled the crossbar with a fine header from Jose Gaya's cross, and Suarez failed to control a pinpoint pass from Andres Iniesta two minutes later.
Valencia looked sharp on the counter-attack and seemed the more likely to break the deadlock, with Cillessen again called into action to deny Rodrigo.
Coutinho replaced Gomes at the break to give Barca more of a threat going forward and the decision paid off four minutes into the second half. Suarez drove into the penalty area down the left and crossed towards the far post, where Coutinho stretched to turn the ball back across goal and into the left-hand corner.
The goal seemed to sap the belief from the Mestalla crowd and the Valencia players and Suarez nearly curled home a second Barca goal after a sustained period of possession for the visitors.
Messi saw a shot saved by Domenech and Martin Montoya blocked Jordi Alba's rebound wide, although the former Barca man was lucky not to concede a penalty, with the ball clearly striking his arm.
Simone Zaza fired a good chance over the bar as Valencia pushed forward for a lifeline, with Rakitic twice shooting wide on the break as the home side began to look exposed at the back.
Gaya thought he had halved the deficit with quarter of an hour left but Cillessen produced one of the saves of the season to block his effort from point-blank range and turn the ball past the post.
The stop proved pivotal as, with eight minutes left, Suarez stole back possession and fed Rakitic, who fired home from just inside the box to safeguard the win.
The only concern for Barca will be the sight of Pique in obvious discomfort after going off late on to be replaced by €11.8m man Yerry Mina, who made his debut.
