Heavy rain in Klang denied either side a chance to end the tournament with six successive wins as Nepal finished top of the seven-team standings with 11 points, the same as Singapore, but with superior run-rate.
Malaysia defeated China by 10 wickets in Bangi to claim third spot on a better net run-rate from Thailand after both teams wound up with seven points.
The victory enabled Malaysia to join Nepal and Singapore in qualifying for the Asia Regional Finals from this tournament. The United Arab Emirates, Qatar and Kuwait qualified from the Asia Qualifier 'A' in April.
Nepal's Sandeep Lamichhane emerged as the tournament's highest wicket-taker after claiming 4/16 to take his tally to 24 as Singapore were bowled out for 81 in 17.3 overs at the Bayuemas Oval.
Sompal Kami (2/20) reduced Singapore to 15/2 after removing Aritra Dutta (4) and Chaminda Kumarage (6) before Lamichhane dismissed Singapore captain Chetan Suryawanshi for 9.
Surendran Chandramohan attempted to revive Singapore in a fourth-wicket stand of 28 with Manpreet Singh but after Basant Regmi had Surendran bowled for 25 following a brief rain interruption, Singapore lost their last six wickets for the addition of 21 runs.
Surendran, though, had the consolation of becoming the tournament's highest run-scorer with 148 at an average of 29.60.
Nepal only faced three balls, with Shoaib Razzak having Anil Kumar Shah out for nought, before play was halted again at 1/1 due to heavy rain.
"It has been a well-disciplined, clinical tournament for us with everybody up to the mark irrespective of our opponents. We had to play to our standards and glad that we were able to do that," said Nepal captain Paras Khadka.
"We can't control the weather and 82 is a score we would have backed ourselves to get. This is just the first stage, the second round won't be as easy as this round. Hopefully we can continue to show the form we have shown this past week.
Earlier, there were concerned looks in the Malaysian camp after overnight rain and cloudy conditions in the morning left the UKM Oval outfield damp.
After using a leaf-blower to dry the ground, play eventually commenced two hours after the scheduled start with the contest reduced to 11 overs a side.
Malaysia won the toss and elected to field, bowling China out for 30 runs in 10 overs before reaching their target in 18 balls.
Only Chen Jinfeng (21) provided any resistance for China as Pavandeep Singh, Anwar Rahman and Abdul Rashid Ahad picked up two wickets each before man-of-the-match Sivanantha Krishnan wiped out the tail with three wickets for no runs.
Shafiq Sharif (19) and Anwar Arudin (11) then combined for 31 runs to steer Malaysia to their third win in six matches and a place at the Asia Regional Finals.
"We just needed to win this match to qualify for the next stage and even though the start was delayed, we were ready from a psychological point of view to do what was needed," said Malaysia captain Ahmad Faiz Mohammed Noor.
"We bowled very well today and we're very happy to have qualified for the next stage, for which we have to start preparing immediately."
Bhutan clinched fifth spot on four points after beating Myanmar by 39 runs at the Bayuemas Oval.
Kumar Subba scored 45 off 59 balls while Jigme Singye chipped in with 20 as Bhutan reached 105/8 in 20 overs. Ko Ko Li Thu was the pick of the Myanmar bowlers after taking three wickets for 13 in four overs.
Singye returned to capture three wickets for six runs and help bowl Myanmar out for 66 in 17 overs, Ko Ko Lin Thu top scoring with 17.