Morbidelli, who won the Moto2 championship in 2016, moved up to the premier class in 2018.
He is the first rider from Valentino Rossi’s VR46 Riders Academy to stand on the MotoGP podium.
The academy was created in 2014 by Rossi and nurtures the talents of young Italian motorcycle riders.
Riders from the academy grow up training together and are also supported individually through tailored physical fitness programs.
The academy began with six talents, including Morbidelli and Pecco Bagnaia, who now both ride in MotoGP.
Morbidelli, who qualified third at the Czech Republic MotoGP, launched from the grid to take the lead around Turn 1.
He led the race for the next 12 laps until South African rookie Brad Binder passed him on Lap 9.
Binder made a run for it and eventually created a gap that Morbidelli could not catch.
However, the young Italian held on to second position as a battle for third emerged behind him.
Frenchman Johann Zarco managed to maintain third position despite being hit with a Long Lap Penalty due to an on-track incident that occurred on Lap 9 with Pol Espargaro.
The two riders made contact around Turn 2 and Espargaro slid off his bike, which eventuated in a penalty for Zarco.
The results from the weekend see Morbidelli move up to equal-third position in the championship on 31 points behind his teammate Fabio Quartararo, who leads on 59 points, and Maverick Vinales, in second position on 42 points.
“It feels amazing…I’m overwhelmed right now,” Morbidelli said about his first podium following the race.
“I saw that Brad was catching up... I said I won’t do anything silly and I will just try to bring the bike to the end and catch my first podium.”
Catch the fourth round of the MotoGP on August 16, 10:00 pm AEST, at the Austrian MotoGP.
Czech Republic GP Results
- Binder (RSA) - Red Bull KT
- Morbidelli (ITA) - Petronas Yamaha
- Zarco (FRA) – Real Avintia
- Rins (SPA) - Suzuki Ecstar
- Rossi (ITA) - Monster Yamaha
- Oliveira (POR) - Red Bull KTM Tech3
- Quartararo (FRA) - Petronas Yamaha
- Nakagami (JPN) - LCR Honda
- Miller (AUS) - Pramac Ducati
- A Espargaro (SPA) - Aprilia Gresini
- Dovizioso (ITA) – Ducati
- Petrucci (ITA) – Ducati
- Crutchlow (GBR) - LCR Honda
- Vinales (SPA) - Monster Yamaha
- Alex Marquez (SPA) – Repsol Honda
- Rabat (SPA) - Reale Avintia Ducati
- Smith (GBR) Aprilia (test rider)
- Bradl (GER) Repsol Honda
DID NOT FINISH
Mir (SPA) – Suzuki Ecstar
Lecuona (SPA) - Red Bull KTM Tech3
Pol Espargaro (SPA) – Red Bull KTM Factory