Although they were hanging on at the end, Stuart McCall's side moved to within a point of Aberdeen in second place, and are the same margin away from a place in Europe next season.
"Our first-half performance merited victory," the Motherwell manager said. "We said we had to win our last three games to ensure we finished in second place and that's one down with two to go. The second half was a bit of a struggle for us, but Lee [Hollis] had only one save to make."
The talking point, undoubtedly, was the McManus goal after 35 minures. "There was a foul on Dave Mackay in the build-up," St Johnstone manager Tommy Wright said emphatically. But it was what happened next which left Fir Park in confusion.
As the Motherwell central defender's header from a corner headed for the net it was punched clear by Steven Anderson. Referee Kevin Clancy's instinct seemed to be that the ball hadn't crossed the line but his nearside official, Andrew McWilliam, thought differently.
"My first reaction was penalty kick and they're down to 10 men, which I got quite excited about," said McCall. "Then I was even more excited when I saw the linesman sprinting up to the halfway line and I realised - or at least I thought I did - he'd given a goal."
Anderson was booked in the aftermath and the goal proved to be the winner, although as Wright and McCall both noted the visitors dominated the second half and Motherwell had an excellent late save from Hollis to thank for collecting all three points.
It was obvious from the way Motherwell set about their business that they intended to distance themselves from the previous weekend's 5-1 defeat at Tannadice. The best of three decent chances in the first ten minutes fell to James McFadden, but with plenty of time near the penalty spot he shot weakly at Alan Mannus.
Saints were still struggling to get a foothold in the game by the time Lionel Ainsworth put the home side ahead in the 21st minute. Keith Lasley started the move, it was carried on by John Sutton and McFadden, leaving Ainsworth to curl in a cross which deceived Mannus and dropped into the net behind him.
Though slightly fortuitous, it was no more than Motherwell deserved, but their lead was short-lived. David Wotherspoon won a corner on the right, took it himself, and it was met squarely by Saints captain Mackay.
Given that this had been a rare Saints attack the home side were entitled to feel aggrieved, but they regained the initiative with their bizarre goal 10 minutes from the interval.
Whether or not the ball was actually over the line when his St Johnstone counterpart, Anderson, stuck out his fist, became a matter of some contention. Eventually referee Clancy awarded the goal before booking the Saints defender.
The visitors were more ambitious in the second half, with their best efforts coming from Michael O'Halloran and Wotherspoon, who both just missed the target with good shots.