Less than 24 hours after being given permission to speak to Bristol City, McInnes saw his side consolidate their top-six position in the Scottish Premier League thanks to strikes from Francisco Sandaza and Dave Mackay.
Sandaza linked brilliantly with Cillian Sheridan to net his seventh goal of the season in the early stages and Mackay finished well in the 65th minute after Inverness failed to clear a Jody Morris cross.
McInnes, who acknowledged the home fans' acclaim before quickly moving down the tunnel after the final whistle, is set to hold talks with City in the coming days.
But, if he is to leave McDiarmid Park, he will depart with the team in a healthy state.
Sheridan and Sandaza now have 11 goals between them and fashioned the opener from nothing, although the Irishman soon went off injured.
And Frazer Wright returned from injury to superbly marshal a defence that has now kept seven clean sheets.
The opener came in the 13th minute after Sandaza collected the ball just inside the Inverness half and fed Sheridan on the left wing with the visiting defence on the back foot.
Sheridan returned the ball to his strike partner on the edge of the area with a lofted pass and the Spaniard chested it down, shrugged off a defender and shot high into the net with his left foot.
Sandaza engineered another chance when his skill took him away from two men following Liam Craig's low cross but Ryan Esson was quickly off his line to block the striker's close-range effort.
The forward pairing was split up in the 20th minute when Marcus Haber replaced Sheridan.
Inverness were struggling to break through and Andrew Shinnie took a heavy touch when Richie Foran's header found him in space in the box.
Caley Thistle midfielder Greg Tansey fired in two decent long-range strikes but neither forced Peter Enckelman into action and Shinnie curled just over from a difficult angle.
Enckelman made his first save to guide David Proctor's header over following a corner but St Johnstone survived the spell of pressure and should have gone further ahead in injury-time after a sweeping move from deep inside their own half.
Mackay and Chris Millar linked up brilliantly on the right to set up Haber 12 yards out but the striker scuffed his shot against the post and Thomas Piermayr blocked as Craig followed up.
The Perth side came out eager to add to their tally and Esson got down well to save Mackay's drive after Millar had fed his forward run.
Inverness brought on Shane Sutherland and Aidan Chippendale but they should have been further behind in the 62nd minute when Kevin Moon ran unmarked on to Craig's cross, however the midfielder sliced his first-time effort over.
Moon was soon replaced by Murray Davidson, making his first appearance since August after recovering from a knee injury, and Saints almost immediately doubled their lead.
Sandaza put Esson under pressure from Morris's right-wing cross and the ball fell for Mackay, who sent a first-time left-footed effort into the bottom corner from 14 yards.
Foran almost pulled one back with a brilliant 20-yard strike but Enckelman pushed it on to the bar and over, and Saints held on to their lead comfortably.
Their fans will now hope they can also retain the services of McInnes after Saints moved one point behind Celtic in the SPL.