Chasing 230 for victory, Ireland had reached 27 for 0 when Joyce - who scored a match-winning century in Thursday's win for Ireland - stopped in the middle of the pitch after feeling the ball was well over the boundary. However, the Afghanistan fielder insisted he had prevented the boundary and claimed the run out of Ireland's talismanic opener.
A lengthy discussion ensued between the umpires and eventually Joyce was adjudicated out - the umpires having to take the word of the fielder - much to the chagrin of the Irish camp.
William Porterfield, Sean Terry and Stuart Poynter all went cheaply as Ireland were reeling on 67 for 4. Kevin O'Brien (34) and Paul Stirling (31) added a fifth wicket stand of 63 to put Ireland back in contention at 130 for 4.
Pulled by Mohammad Shahzad
However, both were dismissed in the space of seven balls and after that Ireland wilted to be all out for 150, losing six wickets for 20 runs. Leg-spinner Rashid Khan made it a day to remember for him personally as he claimed 4-21; Khan earlier top-scoring with the bat as the visitors posted 229 for 7 from their 50 overs.
Afghanistan's innings was built mainly on a couple of late partnerships after Ireland's bowlers dominated the early exchanges. Peter Chase (2-59), Paul Stirling (1-24) and Barry McCarthy (1-40) were all on target as the batsmen found the going tough; however Andy McBrine (2-29 from 10) was the pick of the attack as the Afghans slumped to 90-5 at the half-way point.
Peter Chase bowling
Rahmat Shah provided the resistance in the top half as he made a valuable 48 (4 fours) before a stand of 54 between Nabi and Khan began the fightback.
The former hit 5 fours and a six before dinking a catch to Peter Chase immediately after bringing up his half century, but Khan took advantage of a couple of missed chances as the innings gained late momentum.
An otherwise excellent performance in the field was spoiled somewhat as Porterfield's men spurned two opportunities to account for man-of-the-match Khan and he made them pay with an unbeaten 60 off just 44 balls (5 fours, 2 sixes).
Six hit for Mohammad Nabi
In all, 44 runs came off the final three overs- 16 of them from the last three deliveries- as Ireland were made to pay for their wastefulness.
In the end it was to be a gap the home side couldn't close and while they will leave Stormont with a slightly bitter taste in their mouth, Porterfield's men have a chance to tie it up when the fifth and final match gets under way on Tuesday.