The game was an even contest to begin with but the home side slowly began to assert their authority with James McFadden and Iain Vigurs both forcing early saves from Alan Mannus.
And Motherwell got a deserved breakthrough in the 21st minute after some neat play from former Everton striker McFadden.
The 31-year-old fed Lionel Ainsworth, who somehow managed to rifle the ball past Mannus and into the top left corner of the net from a very acute angle on the right.
But St Johnstone hit back just six minutes later, David Wotherspoon crossing for David Mackay to score his third goal of the season with a header.
Motherwell re-established their lead before the end of the half with a header of their own when Iain Vigurs crossed for former Celtic defender Stephen McManus to head the ball goalwards.
His header was cleared away, but after pausing for thought, referee Kevin Clancy ruled that the ball had crossed the line.
Michael O’Halloran and Wotherspoon had early chances in the second half but were unable to trouble Lee Hollis in the Motherwell goal.
Saints leading goalscorer Stevie May went close with a header as the half wore on but was also unable to find the target.
Henri Anier, a second-half substitute for McFadden, had an opportunity to extend the home side’s advantage but saw his left-footed effort from outside the area blocked.
Gary Miller almost grabbed a point for Saints with a long-range effort but Hollis was equal to the task as Motherwell held on to stay third and move a point behind Aberdeen in second.