Friday’s second 70-minute session at the Buddh International Circuit was delayed by around 45 minutes due to some logistical issues affecting the beginning of the earlier Moto3 FP2.
Once action got underway, Marini guided his year-old Ducati to a 1m44.782s to lead Pramac’s Jorge Martin by 0.008 seconds.
In a first for the 2023 season, both factory Honda riders have secured a place in Q2 for Saturday’s qualifying, after Marc Marquez was fourth and team-mate Joan Mir 10th.
Joining them will be Yamaha’s Fabio Quartararo, who cast aside his difficult FP1 to secure a place in Q2 for the first time since the Austrian GP weekend.
The new Buddh layout continued to prove tricky for riders when second practice got underway, as KTM’s Jack Miller crashed at Turn 12 in the opening moments.
The Australian struggled for pace all afternoon and was only 18th at the chequered flag.
FP1 pacesetter Marco Bezzecchi on the sister VR46 Ducati set the initial pace at 1m46.674s, before Aprilia’s Aleix Espargaro leaped up to top spot with a 1m46.387s inside the first 10 minutes of the session.
Jorge Martin then went top with a 1m46.182s on his Pramac Ducati, before Bezzecchi re-established himself with a 1m45.993s with 15 minutes of the session gone.
Marini’s session was briefly interrupted by a crash at the half-hour mark as he made his way into the difficult Turn 1 right-hander.
This wouldn’t throw him off his stride, however, as he rebounded to fire in a 1m44.782s in the final moments of second practice to secure top spot.
He took over from Martin, whose 1m44.790s put him top of the standings briefly just a few moments earlier, and would be good enough to keep him second.
Aleix Espargaro rounded out the top three a further 0.043s adrift, with Marc Marquez fourth ahead of Bezzecchi.
Maverick Vinales, who led the way for a time in second practice, was sixth on the sister factory Aprilia ahead of world champion Francesco Bagnaia on the factory Ducati.
Quartararo held onto eighth ahead of Pramac’s Johann Zarco and Honda’s Mir.
The 2020 world champion was briefly knocked out of the Q2 places as KTM’s Brad Binder jumped up to fourth with his final effort.
However, a yellow flag in the third sector after LCR Honda’s Takaaki Nakagami crashed at Turn 8, meant Binder’s lap was cancelled.
This dropped him down to 12th behind Gresini’s Fabio Di Giannantonio, with Alex Marquez on the sister Gresini Ducati, Yamaha’s Franco Morbidelli and Tech3’s Augusto Fernandez – who also had a top 10-worthy lap deleted at the end of the session – rounding out the top 15.