The club will sport the Perth-based ambulance charity's helicopter logo on their shorts.
Chairman Steve Brown said the move was to help "put something back into the wider community".
The club will also offer SCAA the use of facilities at McDiarmid Park, and hold collections at key matches.
Team captain Dave Mackay said players were "immensely proud" to wear the SCAA logo.
He said: "Part of this charity's life-saving work is flying to sporting accidents all across Scotland.
"None of us know when we might need their services - we're just glad that they're there. The guys are honoured to be asked to support SCAA in this way and are extremely happy to do so."
Mr Brown added: "St Johnstone is very proud to be based in Perth, but we enjoy a Scotland-wide profile. The same goes for Scotland's Charity Air Ambulance, which is based at Perth Airport but flies emergency missions all across the country.
"By offering the charity exposure on our team shorts we feel we are helping to put something back into the wider community which has supported us for so many years. SCAA does a truly amazing job and their life-saving service is there for all of us - it's the ideal charity partner for St Johnstone."
St Johnstone FC is to carry the logo of Scotland's Charity Air Ambulance on the club's kits in the coming season.