Booth and Gillingham boss Jepson were a lethal partnership in Huddersfield's promotion winning side of the mid-1990s and are still friends.
Jepson even turned out for Booth's testimonial match earlier this season but had lost the battle between old pals inside eight minutes.
Luke Beckett put Town ahead on three minutes and Booth added a second soon after with a wonderful header from an improbably tight angle to convert Chris Brandon's cross.
Gillingham's defenders appeared to be unsighted for both goals by a very strong sunlight during the first half - made worse by keeper Romain Larrieu's decision not to wear a cap.
Gary Mulligan went closer for the visitors with a header from Nicky Southall's cross on 19 minutes but was denied by a great save from Huddersfield keeper Matt Glennon.
That was the closest Gillingham came in a poor first half for the visitors. But they perked up after the break and got back in it at 2-1 when Southall and Mulligan combined again.
Southall's teasing cross from the right on 70 minutes found Mulligan unmarked at the far post and he headed into the roof of the net from a close range.
Huddersfield defender Nathan Clarke, making his first start for two months following a knee injury, landed badly while trying to reach Southall's cross and had to be substituted.
Gillingham's resurgence was snuffed out seven minutes from time by Booth when he applied the finish to Beckett's flick on from a Danny Schofield corner.
Schofield, always inventive down the left flank, could have added a gloss to the scoreline in stoppage time with a long-range blast that flew just wide.
Huddersfield have now won three of their last four games - a run that makes their slim play-off hopes more credible.
Gillingham, who beat promotion contenders Tranmere last week, were disappointing and have now won just once in their last seven games.