"There is absolutely no panic," said Arthur.
"This was just a practice match and it didn't go our way.
"I think if the coin had fallen the other way and had we bowled first, it would have been different.
"Our bowlers had a decent workout, but the only concern is that the top order still needs some runs," added the coach after seeing another below-par effort from his batsmen who managed just 192 against Ireland on Monday.
The game was interrupted for almost 10 minutes during the South African innings after the players complained about the state of the pitch, with the batting side 56 for 3 at that stage.
"I don't think we are going to play on such pitches in the main competition, if my information about the pitches is right," said Arthur.
"I think it's certainly going to be a bowl-first competition, but the toss is not going to be as crucial as it was today."
As the day wore on the pitch became easier to play with Pakistan batting as if it was the easiest job in the world, surpassing South Africa's total with more than five overs to spare.
"It was a tale of two pitches," added Arthur.
"When we batted it was wet and difficult. It dried up later and batting became easier. It was of variable bounce when we started, but awesome to bat on later in the match."
Four South African batsmen made decent starts with Loots Bosman top-scoring with 53, Ashwell Prince 35, Jacques Kallis 29, and Mark Boucher 22, but none went on with it.
The Pakistani bowling attack, missing Shoaib Akhtar and Mohammad Asif through injury, did their job well with seamers Mohammad Sami and Umar Gul, and off-spinners Mohammad Hafeez and Shoaib Malik grabbing two wickets apiece.
Pakistan's batting flourished on the improving pitch with Younis Khan (79), opener Mohammad Hafeez (49) and Mohammad Yousuf (48 not out) seeing their side to a comfortable win.
Pakistan open the tournament in the first match against the West Indies in Jamaica on Tuesday, while South Africa open their campaign against the Netherlands on Friday in St Kitts & Nevis.