Herta had vaulted to the top of the session with a with a 59.7104s lap, which was eclipsed by Will Power delivering a lap 0.03s quicker before improving to a 59.6058s time.
But Power, a nine-time St. Petersburg polesitter, had got sideways in Turn 9 on his best lap – and that opened the door for team- mate McLaughlin, who had earlier headed the second free practice session at the Florida street course.
An error-free lap from McLaughlin, who finished second in his initial qualifying group, handed him enough to beat Power by 0.1237s to clock a 59.4821s, an average of 108.940mph around the 1.8-mile course.
Power had led McLaughlin in a Penske 1-2 in their Group 2 session to book a place into the second phase of qualifying – which he also headed from Herta and McLaughlin.
Herta collected the third fastest time overall, having secured his own Q2 berth by topping the opening group session ahead of Graham Rahal and Rinus VeeKay.
VeeKay ensured three Chevrolets in the top four with a 59.8102s, the Ed Carpenter Racing driver beating Andretti newcomer Romain Grosjean and Meyer Shank Racing’s Simon Pagenaud.
The Ganassi cars failed to make the cut into the Fast Six, albeit stronger than in Friday’s practice; Scott Dixon, Marcus Ericsson and Alex Palou finished up seventh, eighth and 10th respectively.
Dixon admitted he had clipped the wall on Turn 9 entry while on primaries and then mistimed his flying on the improved-grip softer compound tyres.
Also eliminated at this stage was Penske’s Josef Newgarden, as the two-time St. Petersburg winner qualified ninth ahead of Palou – telling NBC he was fighting a couple of issues and had also been struggling with traffic.
Rahal qualified 11th, while rookie Kyle Kirkwood also made it into the Q2 session, but was kicking himself at making a mistake at the final corner at the start of his flying lap.
Kirkwood confessed he then pushed too hard in his AJ Foyt Racing car and brushed the Turn 9 exit wall, but was reasonably satisfied to wind up as fastest rookie – and will start Sunday’s race from 12th.
Arrow McLaren SP’s Pato O’Ward bent his left-rear toe-link on the wall at Turn 9 during Q1, ending his chances to fight for pole early.
Jimmie Johnson was last in the first group but had his best lap impeded by rookie David Malukas in the #18 Dale Coyne Racing car, the youngster getting penalised as a result.
A puzzled Alexander Rossi was a surprise failure to graduate into Q2, as was Helio Castroneves of Meyer Shank Racing.