It was a vital win for the Saddlers who now have four successive away games.
But it was a bitter blow for the Gills who had only lost one of their previous five away games.
Pedro Matias lifted Walsall's hopes in the first half with a superb 35th minute goal only for Gillingham to hit back with a 48th minute penalty equaliser from on-loan Wayne Brown.
Gillingham were under a great deal of first-half pressure with Paul Merson often the mastermind of Walsall's attacks.
Goalkeeper Bossu, who made his debut for Gillingham, enjoyed mixed fortunes. The 20-year-old Frenchman, who was only signed a month ago from Hayes, made a superb save from Walsall's on-loan defender Baird.
He then experienced several anxious moments as he struggled with some high crosses but he was eventually beaten in the 35th minute following a five-man move which ended with Jamie Lawrence playing the ball back for Matias to score with an accurate low left-footed shot to the right of Bossu.
Danny Spiller raised Gillingham's hopes just before the break with a 30-yard shot which whistled just over the bar.
Hessenthaler brought himself on for the second half and within three minutes the Gills were on level terms.
Vinny Samways was alleged to have handled the ball and Brown converted the penalty with a low left-foot shot to the left of James Walker.
Gillingham were often the more dangerous side in the second period when inspired by Hassenthaler.
But the Gills' 38-year-old boss was far from happy afterwards when he said: "It was a freak goal and it was my first own goal.
"I thought we deserved a point with our second-half performance."
Walsall's boss, Colin Lee, admitted: "Our heads could have gone down after the penalty but we battled back to score a very important win."
Walsall: Walker, Baird, Emblen, Ritchie, Aranalde, O'Neil, Lawrence, Samways, Matias, Merson, Leitao. Subs: Kerr, Bazeley, Osborn, Birch, Burton.
Gillingham: Bossu, Wayne Brown, Hope, Cox, Nosworthy, Perpetuini, Saunders, Smith, Spiller, Benjamin, Sidibe. Subs: Hills, Ashby, Hessenthaler, Tommy Johnson, Leon Johnson.
Referee: F Stretton (Nottinghamshire)
Attendance: 6,395