Production will be limited to just 100 cars here.
The feature will be a no-cost option, the automaker said.
Pricing is not confirmed, but it likely will be around around $199,995 for the manual version, Aston Martin spokesman Matthew Clarke told Edmunds.
Aston Martin dealers will begin taking deliveries of the manual V12 Vantage S in the third quarter of 2016.
Buyers can choose from either the manual transmission or the seven-speed automatic transmission when ordering their car.
The 2017 V12 Vantage S is equipped with a 6.0-liter V12 engine.
Zero-to-60 mph time is pegged at 3.9 seconds. The car reaches 205 mph with either transmission.
Aston Martin said the new manual transmission features "a classic dog-leg first gear position" that ensures the gears used most frequently are located in a double "H" pattern, similar to a conventional six-speed manual.
"At a time when manual transmissions have almost entirely disappeared in high-performance cars, this makes the manual V12 Vantage S a very special car indeed," said Ian Minards, Aston Martin director of product development, in a statement.
The new transmission also features AMSHIFT.
With this system, the driver can mimic the technique of heel-and-toe downshifts, along with full-throttle upshifts.
It can "be used in all driving modes, but is especially effective in Sport, with the sharper throttle response and louder exhaust note really emphasizing the downshift throttle blip for maximum excitement," the company said.
The V12 Vantage S also features a new infotainment and satellite navigation system.
A new Sport-Plus Pack option includes a choice of five body colors with no-cost optional accent colors on the exterior.
Edmunds says: Contact your Aston Martin dealer now if you want to get in line for a car that's sure to be a winner with purists.