The Uruguayan star, 14 goals from midfield last season, hit both goals as we strectched our pre-season record to four wins in four at the Priestfield Stadium.
He curled home a second-minute free-kick as the home side organised their defensive wall and, after Gills had levelled, headed home Darren Anderton's corner for the winner after 75 minutes.
Poyet was the star of our first half performance alongside Mauricio Taricco and the South American pair carved out a number of chances with their clever combinations down the left flank.
They were the source of chances for Diego Bortolozzo (a weak shot after 24 minutes), Steve Carr (drove wide after 31) and Taricco himself curled wide after a one-two cut the Gills open just before the break.
But Gillingham also had their moments. Paul Shaw brought the best out of Lars Hirschfeld after six minutes, tipping over his 25-yarder at full stretch and Rod Wallace might have done better when Shaw found a hole in an otherwise tight back three after 26 minutes.
Carr, back in pre-season action after missing our last three friendlies, looked to push on more and more and played for 53 minutes before being replaced by Oyvind Leonhardsen.
The second half was all about our possession but it took until the 61st minute for the next strike as Anderton's rocket flew just wide.
Gillingham hit back though and Kevin James fired a stinging warning to Hirschfeld's fingers after 64 minutes before equalising three minutes later.
There was a touch of fortune about it as James, in space, let rip from 30 yards only for his shot to clip Goran Bunjevcevic's outstretched leg and drift beyond the reach of Hirschfeld.
Our response was swift. Substitute John Sutton floated in a cross met by Poyet that Jason Brown acrobatically tipped over but the midfielder had the last laugh from Anderton's corner, rising high to power his header home from eight yards.
Spurs: Hirshfeld, Carr (Leonhardsen, 53), Taricco (Jackson, 71), Bunjevcevic, Doherty (O'Donoghue, 45), Richards, Bortolozzo (Ricketts, 45), Poyet (Etherington, 80), Anderton, Iversen (Sutton, 61), Barnard.
Paul Miles at Priestfield Stadium
Gus Poyet got off the mark for the summer with a double in our latest friendly outing at Gillingham on Saturday.