paths = {{{348.488, 132.622}, {336.333, 63.6857}, {394.365, 24.5422},
          {39.3603, 78.1653}, {109.094, 84.2662}, {170.317, 50.3295},
          {195.403, 115.68}, {263.324, 132.615}, {316.947, 177.61},
          {381.382, 150.259}, {49.8526, 164.812}, {41.3217, 95.3342},
          {11.7384, 158.776}, {65.3616, 113.781}, {5.35985, 77.728},
          {18.7165, 9.01408}, {358.715, 372.961}, {394.767, 312.96},
          {340.367, 268.907}, {313.016, 333.343}, {269.92, 388.503}}};

r = 3;
torus[{u_, v_}] := {Cos[u]*(Sin[v] + r), Sin[u]*(Sin[v] + r), Cos[v]}

Needs["VariationalMethods`"]
eq = EulerEquations[Sqrt[Total[D[torus[{u, v[u]}], u]^2]], v[u], u];

geodesic[{{u1_, v1_}, {u2_, v2_}}] := Module[{start, g, sol},
  If[u2 < u1, Return[geodesic[{{u2, v2}, {u1, v1}}]]];
  sol = ParametricNDSolve[Flatten[{
      eq, v[0] == v1, v'[0] == a
      }], v, {u, 0, u2 - u1}, {a}];
  start = a /. FindRoot[Evaluate[(v[a][u2 - u1] - v2 /. sol)], {a, 0}];
  g = v[start] /. sol;
  Function[t, {u1 + t*(u2 - u1), g[t*(u2 - u1)]}]
  ]

LocatorPane[
 Dynamic[pts],
 Dynamic[ParametricPlot[Evaluate[geodesic[pts][t]], {t, 0, 1},
   PlotRange -> {{-π, π}, {-π, π}}, Axes -> True,
   AspectRatio -> 1/r]]]

Show[
 ParametricPlot3D[
  torus[{u, v}], {u, -π, π}, {v, -π, π},
  PlotStyle -> White, ImageSize -> 500],
 ParametricPlot3D[Evaluate[torus[geodesic[pts][t]]], {t, 0, 1},
  PlotStyle -> Red]
 ]

Clear[geodesicFindMin]
geodesicFindMin[{p1_, p2_}, nPts_: 25] :=
 Module[{approximatePts, optimizeOffset, optimizeOffsets, direction,
   normal, pathLength, optimalPath, interpolations, len, solution},
  direction = p2 - p1;
  normal = {{0, 1}, {-1, 0}}.direction;

  approximatePts = Join[
    {p1},
    Table[
     p1 + i*direction/(nPts + 1) + optimizeOffset[i]*normal, {i,
      nPts}],
    {p2}];

  pathLength = Total[Norm /@ Differences[torus /@ approximatePts]];

  {len, solution} =
   Quiet[FindMinimum[pathLength,
     Table[{optimizeOffset[i], 0}, {i, nPts}]]];
  optimalPath = approximatePts /. solution;

  interpolations =
   ListInterpolation[#, {{0, 1}}] & /@ Transpose[optimalPath];

  Function[t, #[t] & /@ interpolations]
  ]

LocatorPane[
 Dynamic[pts],
 Dynamic[ParametricPlot[Evaluate[geodesicFindMin[pts][t]], {t, 0, 1},
   PlotRange -> {{-π, π}, {-2 π, 2 π}}, Axes -> True,
   AspectRatio -> 2/r]]]

Show[
 ParametricPlot3D[
  torus[{u, v}], {u, -π, π}, {v, -π, π},
  PlotStyle -> Directive[White], ImageSize -> 500],
 ParametricPlot3D[Evaluate[torus[geodesicFindMin[pts][t]]], {t, 0, 1},
   PlotStyle -> Red]
 ]