Herta topped the 45-minute session around the 11-turn, 1.786-mile Exhibition Place street course with a best lap of 1m00.5657s.
With rain threatening, the track was busy right from the start of the session as teams tried to get runs in before the showers took hold.
Herta set the early pace at 1m03.5437s before Scott Dixon (Chip Ganassi Racing) and then Romain Grosjean (Andretti) usurped him from the top of the speed chart. Grosjean set 1m02.1538s, which was soundly beaten by team-mate Kyle Kirkwood’s 1m00.8111s.
Local hero Devlin DeFrancesco set an impressive P2 for Andretti, 0.6279s off Kirkwood, with David Malukas (Dale Coyne Racing) leaping up to third.
Despite intensifying rain drops, Arrow McLaren’s Felix Rosenqvist rose to second, 0.2799s slower than Kirkwood, while Graham Rahal jumped to fourth for Rahal Letterman Lanigan Racing.
After 15 minutes, Dixon claimed second place with 1m00.8652s, just 0.05s away from Kirkwood’s best time, with Grosjean and Herta swapping third spot.
Kyle Kirkwood, Andretti Autosport Honda
Photo by: Jake Galstad / Motorsport Images
As the rain abated, Herta took P1 briefly on his next lap of 1m00.6999s but Kirkwood reclaimed it almost immediately with 1m00.5972s, before it swung back again to Herta on 1m00.5657s.
Ganassi duo Marcus Ericsson and Alex Palou – who had a puncture on his alternate-tyre run on Friday – took third and fourth respectively with 15 minutes to go.
Pato O’Ward (Arrow McLaren) was fifth when team-mate Rosenqvist caused the first red flag of the weekend when he put his McLaren into the wall on the exit of Turn 5 with seven minutes to go.
That led to a frenzied final few minutes with 26 cars on track but everyone appeared too preoccupied with finding a gap than improving their laptimes.
Herta went off at Turn 1 and rejoined without incident, virtually matching his quickest lap on his final tour despite almost rear-ending newbie Tom Blomqvist (Meyer Shank Racing). Blomqvist was slowest of the runners, but improved to within 2.1s of the pace.
Callum Ilott (Juncos Hollinger Racing) visited the Turn 8 escape road, but quickly recovered. O’Ward and Rosenqvist (before his shunt) both did likewise at Turn 3 as did the third McLaren driver, Alexander Rossi, at Turn 1.
FP2 result: