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.
The Indian goal had two narrow shaves in sudden-death extra-time when breakaway moves saw Malaysian 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 to 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 comeback 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 Malaysia's 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 the 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.
India, going all out in the last 10 minutes of the regulation period, were rewarded when Yuvraj Walmiki capitalised on a square pass from SV Sunil in the 64th minute.
India's desperate attacks produced the equaliser as Sunil capitalised on a rebound after the Malaysian goalkeeper had padded Sandeep's penalty corner shot.
In the extra time period too, India lived dangerously, allowing the Malaysians time and space to move into the circle before getting the penalty corner that was converted by Raghunath.
Earlier, Pan-American champions Argentina defeated Poland 5-1 to set up a semifinal meeting with Belgium, who outplayed Canada 4-0 in the quarterfinals.
Poland surprised Argentina by taking the lead in the fourth minute through a field goal by Bartosz Zywicka, but the Argentines asserted their authority with three goals in the space of 10 minutes to surge 3-1 ahead at half-time.
Lucas Argento Innocente (13th minute), Pedro Ibarra (22nd) converted a penalty stroke and Rodrigo Nicolas Vila (23rd) scored in open play.
In the second half, Argentina's relaxed play allowed Poland some leeway into their circle, but the South Americans did not concede another goal.
At the other end, Lucas Rafael Rossi (56th minute) and Lucas Martin Vila (68th) made field strikes to round off Argentina's scoring.
Belgium, who were pushed to the second spot in Pool A despite finishing level on points due to India's superior goal difference, packed too much fire for Canada after opening the scoring in the 23rd minute through a penalty corner conversion by Florent van Aubel.
Belgium hammered three goals after the breather with flash field strikes by Thomas Briels in the 49th minute and tournament's top-scorer Tom Boon in the 59th. The other goal came through a penalty stroke conversion by Jerome Dekeyer in the 52nd minute.
Raghunath puts India in semifinals of Champions Challenge
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