Krishna who was heavily marked by the Malaysians in the fixture powered in the right footer in the 71st minute.
It was the timely substitutions in the second spell by national coach Frank Farina that turned the momentum in Fiji's favour.
Napolioni Qasevakatini, Samuela Nabenia and Iosefo Verevou came off the bench to provide the spark in attack after a quiet first spell.
Malaysia goalkeeper Khairul Mat made a few fine saves denying the hosts from taking out maximum points.
Farina said there were many areas to improve on.
He said it was a tough game considering the players participated in the Vodafone Fiji FACT last week.
"I thought we created enough chances to possibly win the game," Farina said.
"It was a bit better in the second half but it is not what I really wanted. We have to be better and need to improve. It was a tough game for the players coming from the Fiji FACT last week.
"They were in camp for only four or five days and had to go to Suva for medical tests."
Fiji will feature in the third round of Oceania's 2018 FIFA World Cup qualifiers next year.
Farina said Roy's goal was a good one.
"There are no excuses but it could have been better," he said.
"The performance today is an indication of tiredness mentally and physically. Malaysia is a good side.
"We have to improve both defensively and attacking wise. It is a work in progress.
"We have ten games coming up for the World Cup qualifiers."
Malaysia coach Datuk Kim said it was a difficult game played in very hot conditions.
"We could have played better but could not hold on to the first half lead," Kim said.
"Overall the boys tried very hard. The tour has given me a lot of ideas before the Suzuki Cup."
Krishna hit the post with a feeble attempt in the 27th minute.
Malaysia scored the opener in the 40th minute after a lapse of concentration in defence as striker Mohammad Yahyah slammed the ball past Benaminio Mateinaqara from inside the box.
Malaysia defeated New Caledonia 2-1 and lost to Papua New Guinea 2-0 on the three match Oceania tour.