Raghunath sent a low shot into the left corner of the goal after a late recovery saw India level 4-4 in regulation period of the action-packed quarterfinal encounter. India will now meet in the semifinal on Saturday hosts South Africa who prevailed over Japan 3-2 in another quarterfinals.
South Africa surged to a three-goal lead before Japan rallied to pull back two in the second half, but the equaliser eluded them.
In the encounter with Malaysia, the Indian goal had two narrow shaves in sudden-death extra-time when breakaway moves saw strikers Faizal Saari and Izwan Firdaus in one-on-one position with goalkeeper PR Sreejesh, but delayed shots by the home side players allowed India stay in the contest.
The Indians were ahead 2-0 before Malaysia struck back to slam four goals. Then, the desperate Indians scored twice in the last six minutes of the regulation period to take the game into extra-time.
Sandeep Singh converted two successive penalty corners, in the sixth and 23rd minutes to give India a 2-0 lead before Malaysia staged a remarkable rally and controlled the game until the 64th minute.
Izwan Firdaus opened Malaysia's scoring with a field goal in the 33rd minute off a pass from Azlan Misron and India were leading 2-1 at half-time.
Misron got he Malaysian equaliser in the 42nd minute as he flicked past a crowded defence and over the Indian goalkeeper.
Malaysia's third goal came on a breakaway move in 46th minute that caught the Indian defence off-guard. Goalkeeper Sreejesh blocked the first shot from Tengku Ahmed who then slammed the board with a firm shot on the rebound.
Misron scored his second goal from Malaysia's second penalty corner, deflecting Amin Rahim's shot in a set-piece execution in the 56th minute.