After a two-hour storm delay in Ipoh before Saturday's 2-2 draw with India, Sunday's kick-off was put back an hour because of further bad weather.
GB wasted no time when the match began, goals from Barry Middleton, David Goodfield and Sam Ward putting them 3-1 ahead.
With 11 minutes left, Japan were only 4-3 down - Tom Carson scoring GB's fourth - but Alan Forsyth settled it.
Japan were considered the outsiders as the lowest-ranked team - at 16th - in the event but claimed a 1-1 draw with hosts Malaysia on Saturday.
GB now have four points from two matches, level with India, who recorded a comfortable 3-0 win over New Zealand earlier on Sunday.
The six-team tournament comprises round-robin, four-quarter matches and, for the first time, video referrals are available.
Defending champions Australia, who drew with New Zealand in their opening match, thrashed Malaysia 6-1 and top the table ahead of Britain and India on goal difference.
Britain's next match is against Malaysia on Tuesday.
The British side will revert to individual nations in June for the World Cup qualifying tournament in London, with England and Scotland in action.
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Great Britain beat Japan 5-3 at the Sultan Azlan Shah Cup in Malaysia.