The England batsman, who walked out of the Ashes tour last year and has undergone months of therapy, scored an unbeaten 79 off 127 balls when the visitors declared at 176-5.
Trott, relishing his role as captain, batted through the morning session in a partnership of 119 with Sam Billings, the Kent wicketkeeper who was drafted into the team for the second innings and marked his Lions debut with a sparky 67-ball half-century.
Billings retired at lunch but Trott batted on, ending with nine fours and a six flicked effortlessly over midwicket off Nono Pongolo. It means that six of the Lions have scored at least a fifty going into the first game against South Africa A which starts in Paarl on Sunday.
The Gauteng XI were 120-8 when the match was abandoned as a draw for safety reasons with an electrical storm approaching fast.