At 07:55, the next American strike from Midway arrived in the form of 16 Marine SBD-2 Dauntless dive bombers of VMSB-241 under Major Lofton R. Henderson. Akagi's three remaining CAP fighters were among the nine still aloft that attacked Henderson's planes, shooting down six of them as they executed a fruitless glide bombing attack on Hiryū. At roughly the same time, the Japanese carriers were attacked by 12 B-17 Flying Fortresses, bombing from 20,000 feet (6,100 m). The high altitude of the B-17s gave the Japanese captains enough time to anticipate where the bombs would land and successfully maneuver their ships out of the impact area. Four B-17s attacked Akagi, but missed with all their bombs.
Akagi reinforced the CAP with launches of three Zeros at 08:08 and four at 08:32. These fresh Zeros helped defeat the next American air strike from Midway, 11 Vought SB2U Vindicator from VMSB-241, which attacked the battleship Haruna starting around 08:30. Three of the Vindicators were shot down, and Haruna escaped damage. Although all the American air strikes had thus far caused negligible damage, they kept the Japanese carrier forces off-balance as Nagumo endeavored to prepare a response to word, received at 08:20, of the sighting of American carrier forces to his northeast.
Akagi began recovering her Midway strike force at 08:37 and finished shortly after 09:00. The landed aircraft were quickly struck below, while the carriers' crews began preparations to spot aircraft for the strike against the American carrier forces. The preparations, however, were interrupted at 09:18 when the first American carrier aircraft to attack were sighted. These consisted of 15 TBD Devastator torpedo bombers of VT-8, led by John C. Waldron from the carrier Hornet. The six airborne Akagi CAP Zeroes joined the other 15 CAP fighters currently aloft in destroying Waldron's planes. All 15 of the American planes were shot down as they attempted a torpedo attack on Soryū, leaving one surviving aviator treading water.
Minutes after the torpedo plane attacks, American carrier-based dive bombers arrived over the Japanese carriers almost undetected and began their dives. It was at this time, around 10:20, that in the words of Jonathan Parshall and Anthony Tully, the "Japanese air defenses would finally and catastrophically fail." Twenty-eight dive bombers from Enterprise, led by C. Wade McClusky, began an attack on Kaga, hitting her with at least four bombs. At the last minute, one of McClusky's elements of three bombers from VB-6, led by squadron commander Richard Best who deduced Kaga to be fatally damaged, broke off and dove simultaneously on Akagi. At approximately 10:26, the three bombers hit her with one 1,000-pound (450 kg) bomb and just missed with two others. The first near-miss landed 5–10 m (16–33 ft) to port, near her island. The third bomb just missed the flight deck and plunged into the water next to the stern. The second bomb, likely dropped by Best, landed at the aft edge of the middle elevator and detonated in the upper hangar. This hit set off explosions among the fully armed and fueled B5N torpedo bombers that were being prepared for an air strike against the American carriers, starting large fires.
At 10:29 Captain Aoki ordered the ship's magazines flooded. The forward magazines were promptly flooded, but not the aft magazines because of valve damage, likely caused by the near miss aft. The ship's main water pump appears to have been damaged, greatly hindering firefighting efforts. On the upper hangar deck, at 10:32 damage control teams attempted to control the spreading fires by employing the one-shot CO2 fire-suppression system. Whether the system functioned or not is unclear but, regardless, the burning aviation fuel proved impossible to control, and serious fires began to advance deeper into the interior of the ship. At 10:40 additional damage caused by the rear near-miss made itself known when the ship's rudder jammed 30 degrees to starboard during an evasive maneuver.
Shortly thereafter, the fires broke through the flight deck and heat and smoke made the ship's bridge unusable. At 10:46 Admiral Nagumo transferred his flag to the light cruiser Nagara. Akagi stopped dead in the water at 13:50 and her crew, except for Captain Taijiro Aoki and damage-control personnel, was evacuated. She burned through the night but did not sink as her crew fought a losing battle against the spreading fires. The damage-control teams were eventually evacuated as well, as was (under duress) Aoki.
At 04:50 on 5 June, Yamamoto ordered Akagi scuttled, saying to his staff, "I was once the captain of Akagi, and it is with heartfelt regret that I must now order that she be sunk." Destroyers Arashi, Hagikaze, Maikaze, and Nowaki each fired one torpedo into the carrier and she sank, bow first, at 05:20 at 30°30′N 178°40′W. Two hundred and sixty-seven men of the ship's crew were lost, the fewest of any of the Japanese fleet carriers lost in the battle. The loss of Akagi and the three other IJN carriers at Midway, comprising two thirds of Japan's total number of fleet carriers and the experienced core of the First Air Fleet, was a crucial strategic defeat for Japan and contributed significantly to Japan's ultimate defeat in the war. In an effort to conceal the defeat, Akagi was not immediately removed from the Navy's registry of ships, instead being listed as "unmanned" before finally being struck from the registry on 25 September 1942.
Shortly afterwards 14 Devastators from VT-6 from the US carrier Enterprise, led by Eugene E. Lindsey, attacked. Lindsey's aircraft tried to sandwich Kaga, but the CAP, reinforced by an additional eight Zeros launched by Akagi at 09:33 and 09:40, shot down all but four of the Devastators, and Kaga dodged the torpedoes. Defensive fire from the Devastators shot down one of Akagi's Zeros.