The union has staged 28 partial strikes since stoppages began on July 13, cutting production by more than 82,000 vehicles valued at 1.7 trillion won ($1.5 billion).
The union narrowly decided in favour of the deal on Monday when 52.9 percent of workers voted to accept proposals that would end a round-the-clock shift system in operation for decades.
The agreement, effective from March 2013, means the introduction of a two-shift daytime work system, ending at 1:00am.
There is also a 98,000 won ($87) increase in basic monthly salary, a performance-based bonus equivalent to five months wages and a one-off payment of 9.6 million won per person.
Hyundai said its 44,000-strong union resumed full production from Tuesday.
With inventories standing at record-low levels, Hyundai plans to spend about 300 billion won to upgrade manufacturing lines, while the union has agreed to an hourly production increase.
Total sales in August were down 4.6 percent from a year ago at 293,924 vehicles. Domestic sales tumbled 30 percent to 35,950 units while 257,974 vehicles were shipped overseas, up 0.4 percent.
Hyundai’s affiliate Kia Motors has seen similar industrial action. Its union plans an eight-hour strike on Wednesday. Since July 13, Kia’s output has fallen by 45,995 vehicles worth 758 billion won.
The two companies together form the world’s fifth largest automaker.