While Thor took down Thanos, however unlike in the movies, it wasn't the God of Thunder who delivered the fatal blow.
In the comics, Thanos' killer was Tarene, aka the Designate. Intended to help humanity reach the next stage of evolution, Tarene was a cosmic being whose power Thanos intended to harness in order to seize control of the universe. After locating the Illumination Stone - which protected him from Tarene's power - Thanos came as close to victory as he ever has, and Thor was only able to defeat him by doubling his strength thanks to a number of enchanted artifacts empowered by Odin. With Thanos downed and the Illumination Stone shattered, it was Tarene who stepped forward to deal the killing blow.
Tarene's power was conveyed by her tears, forcing her to repress the misery of witnessing Thanos' trail of destruction as long as he had the Illumination Stone to protect him. However, once he had been beaten by Thor, Tarene finally allowed herself to cry. Without the Illumination Stone, any evil touched by Tarene's tear burns "as though consumed by the fires of Hell itself." Thanos is immediately engulfed in an inferno, screaming from an intense pain effectively unparalleled in the Marvel Universe. In front of a triumphant Thor, Firelord, and Tarene, Thanos burns alive - an end fitting for Norse mythology, but nowhere family-friendly enough to appear in the MCU. The brutal scene takes place in Thor vol. 2 #25, from Dan Jurgens and John Romita Jr.
While Thanos' rejection by Lady Death explains how he's returned to life many times, his creator Jim Starlin also attempted to retcon several of the Mad Titan's past defeats (including this fiery end) by introducing a group of clones named the Thanosi who had apparently fought and died in Thanos' place. Despite this, the canonicity of Starlin's attempt to reclaim Thanos' narrative is still debated by fans, and the creative team behind Thor #25 clearly intended this Thanos to be the real deal at the time. However, whether this is the original Thanos or a copy of him with all his memories and powers, it's a horrifying way to go, and sees the Mad Titan's immense evil finally come home to roost.
Despite his experience with science and magic, Thanos is generally more at home with the cosmic side of the Marvel Universe than its mythic corners, and he paid the price for crossing Tarene and the Son of Odin. The moment underlined Thanos' growing dependence on cosmic artifacts, and the weak points he created in his plans by relying on power outside himself to get what he wants. Tarene brilliantly emphasizes this point, roasting Thanos alive not with a Cosmic Cube or the Infinity Gauntlet, but with a tear brimming with her own power. Poetically, it's Thanos' own disregard for life that brings Tarene to tears in the first place, making this a moment where Thanos is truly humbled and pays for his evil deeds in a very specific way.
While Thanos has been killed on other occasions - slaughtered by Drax the Destroyer and beheaded by Gamora, to name just a couple - Tarene immolating the Mad Titan remains the R-rated demise that could never be shown on screen, as the Mad Titan suffers an agonizing demise that's as much heard as seen. If Thanos deserves one thing, it's an operatic death that results from his own shortcomings, and Tarene and Thor delivered that several times over.
