John Sutton's well-taken goal got Motherwell off to a flying start and a Ross Forbes penalty increased their lead seconds before the interval.
Defender Shaun Hutchinson made the points safe when he lashed home his second goal in successive games midway through the second half.
Gannon's first seven matches in charge had all been played away from Fir Park as a £250,000 pitch upgrade redirected their Europa League home legs to Airdrie.
The new surface helped Motherwell produce the effective passing game that Gannon demands, and the only black mark on the Motherwell manager's day was a late consolation goal from Jamie Hamill after Motherwell had stopped Kevin Kyle adding to his nine goals from his previous five games.
Both side made changes at full-back with Steven Saunders in for Motherwell and Mark Reynolds moving to left-back in place of Stevie Hammell, while Tim Clancy replaced Garry Hay for Killie.
Motherwell started on the front foot and Cammy Bell was forced into early saves from Hutchinson's header and Jamie Murphy's strike.
Conor Sammon glanced a header just wide at the other end following Steven Old's cross but Motherwell soon took the lead in the 14th minute.
Jim O'Brien slipped the ball into the path of Sutton at the end of a positive run and the striker turned Simon Ford before shooting across Bell with his left foot.
O'Brien turned inside again with good effect as he collected a Mark Reynolds throw and fired a shot which bounced awkwardly in front of Bell, but the Killie keeper managed to turn the ball past the post.
O'Brien did create the second goal when he ran on to a clever pass down the left from Forbes, which took out Old. The Killie right-back brought down O'Brien from behind as the winger ran towards goal and Crawford Allan pointed to the penalty spot.
Forbes placed the penalty just beyond the outstretched arm of Bell to take his tally for the season to five goals.
Old did not reappear for the second half with Danny Invincibile coming on and Hamill dropping to right-back, but the game was almost beyond the visitors by the time the substitute had touched the ball.
Murphy skewed a volley wide following Sutton's chest-down and O'Brien missed a great chance to top his impressive display with a goal.
Some hesitant defending allowed Sutton to run on to Ruddy's kick-out but he delayed his shot and Ford got a challenge in, only for the ball to roll invitingly into the path of O'Brien. However, the former Celtic player curled the ball over from 14 yards.
Invincibile had a chance to give Kilmarnock a much-needed lift when the ball fell for him on the edge of the box but he shot just wide.
O'Brien engineered another shooting chance following a Reynolds throw but Bell caught his 25-yard strike and Well sub Chris Humphrey lobbed a first-time volley just over.
Frazer Wright was fortunate to escape with only a yellow card after kicking Tom Hateley following the Motherwell midfielder's legitimate sliding tackle.
The visitors began to step up a gear and Kyle missed a great chance when he headed over from six yards after Sammon's cross.
Hutchinson soon made Killie pay further when he thundered a volley into the corner from 12 yards in the 68th minute after Clancy had only half-cleared an O'Brien corner.
Motherwell squandered several chances to hurt Kilmarnock on the counter attack and Hamill's clever lob beat John Ruddy following Sammon's deep cross two minutes from time.
Forbes almost restored Well's three-goal advantage when his 25-yard strike bounced off the underside of the bar and just the wrong side of the line.