Nepal reached the target losing eight wickets in 44.1 overs.
Paudel and Karan KC shared a historic partnership of 75 runs for the ninth wicket to steer Nepal to victory.
This is the highest partnership in the history of Nepal for the ninth wicket.
Earlier, this record was held by Sompal Kami and Sandeep Lamichhane.
They had shared a partnership of 41 runs against New Zealand in 2018.
Similarly, KC scored 31 runs off 37 balls hitting two fours and one six.
Nepal’s opener Asif Sheikh contributed 12 runs and Gyanendra Malla returned to the pavilion scoring 21 runs.
Likewise, Kushal Malla made 17 runs while other players failed to score in double digits.
Mark Watt claimed the highest three wickets for Scotland. Chris Greaves took two wickets while McMullen, Safyaan Sharif and Michael Leaask took one wicket each.
Scotland’s Matthew Cross scored 42 runs off 62 balls hitting one six, Brandon McMullen contributed 31 runs while opener Kyle Coetzer and Christopher McBride made 22 runs each.
Sandeep Lamichhane took four wickets for Nepal. Similarly, Karan KC claimed three wickets and Lalit Rajbansi and Kushal Malla took one wicket each.
Earlier on Friday, Nepal thrashed Scotland in the first match by achieving the target of 275 runs.
Nepal, who had defeated Namibia in both the matches, won all the four games of this series.
Nepal is under pressure to win all the remaining eight matches to reach the global qualification of the World Cup.
After this series, Nepal will play against UAE and another series against Papua New Guinea (PNG).
Later, Nepal will play against UAE and PNG at the TU cricket stadium.
Nepal have to win five out of the remaining eight matches to save the ODI status.
