The dist() function will help you find the distance between each pair of points:
set.seed(1)
X<- sample(200:1000,10)
Y<- sample (200:1000, 10)
dat<-data.frame(X,Y)
print(dat)
     X   Y
1  412 364
2  497 341
3  657 748
4  924 506
5  360 813
6  915 596
7  951 770
8  724 987
9  698 501
10 248 815
 dist(dat)
           1         2         3         4         5         6         7         8         9
2   88.05680                                                                                
3  455.50082 437.32025                                                                      
4  531.32664 457.77068 360.35122                                                            
5  452.00111 491.48042 304.02960 642.14095                                                  
6  553.92509 489.64171 299.44616  90.44888 595.91442                                        
7  674.80145 624.62549 294.82198 265.37709 592.56223 177.68511                              
8  696.75893 684.72257 248.21362 520.92322 403.45012 435.15744 314.03503                    
9  317.11985 256.90660 250.37971 226.05530 459.98696 236.88394 369.28309 486.69498          
10 479.89270 535.42226 414.45144 743.27451 112.01786 702.03276 704.43878 506.12251 548.72215
You can then create a matrix that gives you the min distance: 
which(as.matrix(dist(dat))==min(dist(dat)),arr.ind=TRUE)
This is the output:
  row col
2   2   1
1   1   2
Hope this helped.