Ireland, set 174 to win in a match reduced by rain to 31 overs per side, were going well at 45 without loss before losing three wickets for two runs in nine balls.
Philander's figures were the second best by a South African on one-day international debut. Fast bowling great Allan Donald took five for 29 against India at Calcutta in 1991/92.
And afterwards South Africa captain Jacques Kallis said Cape Cobras ace Philander was being groomed to succeed veteran all-rounder Shaun Pollock.
"He's done well back home in domestic cricket and that's the reason he got a call-up here," said Kallis.
"He's a good all-rounder, someone we are going to try to mould along the line of Shaun Pollock. They are big boots to fill, but he started well today (Sunday)," added Kallis, himself one of the world's leading all-rounders.
Earlier Ireland debutant Alex Cusack took three for 15 in four overs as South Africa were held to 173 for four and then finished on 36 not out.
The 26-year-old all-rounder, originally from Brisbane but whose father holds an Irish passport, restricted the Proteas.
They had been on course for a score in excess of 200 in their first match since losing April's World Cup semi-final against eventual champions Australia.
"We knew he could make the step up," said Ireland captain Trent Johnston. "He came out there in tough conditions, against quality batsmen with short boundaries and he hit the top of off-stump. That's all I want.
"He got the rewards with three wickets and then went out and showed us how well he could bat. He's going to be in these Irish colours for a long time and he deserves that," added Johnson, himself Australian-born.
Morne van Wyk's maiden one-day international fifty was the centrepiece of South Africa's total. The opener was appearing in only his second match at this level, four years after making his debut against England at Lord's.
South Africa, after being sent in by Johnston, saw van Wyk (52) and AB de Villiers (40) put on 75 for the first wicket while Kallis made 46.
Openers William Porterfield and Kenny Carroll kept Ireland up with the run-rate.
But Carroll started the slump, unluckily slipping onto his stumps to be out hit wicket off the bowling of Dale Steyn for 21.
"The guys were positive and we had a bit of luck" said Johnston. "But unfortunately it turned against us with Kenny slipping over and then we lost three quick wickets."
South Africa-born Thinus Fourie, surprisingly promoted up the order, fell next when edging Steyn to first slip Justin Kemp.
Lively seamer Philander struck when Porterfield was caught behind and he then clean bowled wicket-keeper Niall O'Brien, who made 52 in Ireland's nine-wicket defeat against India here Saturday, for four.
Ireland had now collapsed to 56 for four and the game was getting beyond their grasp on a cold and dank day.
South Africa's other debutant, off-spinner Thandi Tshabalala, got in on the act with Kevin O'Brien holing out to van Wyk at deep mid-wicket.
Philander ended the match by bowling last man Roger Whelan for nought with a ball to spare.
Earlier, medium-pacer Cusack removed van Wyk, had Herschelle Gibbs caught behind for just two and dismissed Kallis for 46.
South Africa had six survivors from the side that beat Ireland by seven wickets in a World Cup Super Eights match in Georgetown, Guyana in April.
For this match they were captained by Kallis with Graeme Smith recovering from knee surgery in South Africa.
Pollock had been rested from the trip to Ireland while batsman Ashwell Prince had been dropped.
The experienced trio of Andrew Hall, Andre Nel and Charl Langeveldt, all in Ireland, were left out.
South Africa are due to play India in three one-day internationals at Stormont on Tuesday, Friday and Sunday of next week.