Goals by Liam Craig and Nigel Hasselbaink sealed three points for Saints who move into third spot in the SPL table thanks to Ross County's victory over Inverness.
The hosts came close to taking the lead in the 34th minute when Chris Miller fired against a post after latching on to Callum Davidson's cross.
But St Johnstone only had two minutes longer to wait as Craig opened the scoring with a superb strike from all of 35 yards.
Motherwell came close to an equaliser on the stroke of half-time but were denied by keeper Alan Mannus who saved well from a Michael Higdon header, only for Henrik Ojamaa to blast over the rebound.
The second goal arrived just 82 seconds following the re-start when David MacKay fed Hasselbaink who found bottom left-hand corner of the net from 10 yards.
James McFadden could have pulled a goal back for Motherwell while, at the other end, Murray Davidson's 20-yard volley hit the bar.
Craig almost grabbed his second of the day with a shot that flew inches over the bar.
In the end, St Johnstone comfortably posted just a second home victory over Motherwell in 14 attempts and, more importantly, qualified for Europe for a second straight season.