Two first-half goals from James McFadden and Humphrey gave the league runners-up a win in their final home game of the season, and in turn ended County's Europa League chances.
Humphrey set-up Motherwell's lead with what was his first touch of the game, after an impressive run down the right followed by a fine shot across goal left McFadden with little to do at the back post.
County rallied with their first chance of the half soon after, Richie Brittain produced a long-range left-footed effort just wide of Darren Randolph's left post.
And they came even closer just before the break as Ivan Sproule raced through towards goal, but after a heavy first touch Randolph raced off his line to collect at the feet of the Northern Irishman.
County continued to battle for an opportunity before half-time but a poor corner paved the way for a second for Motherwell as Humphrey struck.
The winger slotted the ball calmly under Michael Fraser following an impressive run, to leave County's European hopes hanging by a thread just before the break.
The Staggies continued their charge as they tried to carve out chances but failed to convert, and an awkward fall on the edge of the box for Brittain resulted in the midfielder being stretchered off.
Motherwell looked set for a third when Humphrey and McFadden combined again, the winger played a superb cross in to be headed over the bar by the forward.