Murakami, winner of last year's Iskandar Johor Open in Malaysia on the Asian Tour, carded matching rounds of three-under-par 69 to share top spot with Australian veteran Craig Parry. A total of 12 players teed up for two spots.
"I'm looking forward to my first US Open at Torrey Pines, where I have played many times previously when I was a junior," said the 24-year-old.
His success at qualifying is a huge boost for golf in the Philippines as earlier this season, compatriot Angelo Que earned a ticket to July's British Open.
Former Asian Tour number one Thaworn Wiratchant of Thailand missed out on a top-two spot by one stroke after rounds of 69 and 70 and earned second alternate status via a play-off.
China's Liang Wen-chong, the Asian Tour's Order of Merit champion last season, shot rounds of 69 and 72 to finish three shots outside the qualifying mark while Thailand's Prayad Marksaeng withdrew after an opening 72.
Murakami's success was commendable as he had to deal with a mob of Japanese media and spectators who were following his group that included Japanese teenage sensation Ryo Ishikawa, who carded a two-day total of 143.
In the first round, the bubbly Filipino enjoyed a bogey-free outing with three birdies on the card to end the morning session in fourth place. He roared out of the blocks in style in the afternoon's second round, shooting four birdies in his outward nine.
But with the finish line in sight, a nervous Murakami dropped shots at the 15th and 17th holes to slip out of the lead. However, he steadied his nerves and produced an immaculate chip to three feet for a closing birdie which was enough to seal top spot with Parry.
"My goal today was to avoid bogeys. But I missed putts from seven feet on the 15th and 17th holes and to be honest, I was ready to give up after those two bogeys. So I am really happy to make birdie at the last hole to get a spot," said Murakami.
Further sectional qualifying will be held on June 2, with 12 to be played across the United States and one in England.