Yousuf has remained in Pakistan to be with his wife, who is due to give birth in the next few days after a difficult pregnancy.
''I think they're going to miss Yousuf, he's been such an outstanding player for them,'' Arthur told Reuters.
Yousuf was the leading batsman in the world last year, scoring 1,788 runs in 11 Tests and racking up nine centuries in the process, both records.
Arthur, however, does not think Yousuf's absence will reduce the Pakistani batting line-up to a pushover for the South African bowlers.
''We're expecting Inzamam-ul-Haq to feature strongly, and Younis Khan remains a quality player,'' Arthur said.
Captain Inzamam missed this week's drawn three-day tour match against a Rest of South Africa side in Kimberley with a chest infection. Khan scored 76 in the same game.
''Among their bowlers, Danish Kaneria and Mohammad Asif stand out as threats,'' Arthur said.
Arthur is bemused by the return of fast bowler Shoaib Akhtar to the squad as cover for Umar Gul, who bowled just three overs in the tour match because of an ankle injury.
''That's very interesting, I can't quite believe that he's back in the squad,'' Arthur said.
Shoaib was left out of the original tour party due to lack of fitness, but he reportedly proved his conditioning in a domestic match last week.
Shoaib will, however, not be available to play in the first Test because of travel complications.
Pakistan also have concerns over Shoaib Malik, who also has an ankle problem, and Abdul Razzaq, who has been sidelined for the series with a torn calf muscle.
By contrast, the South Africans are buoyant after rallying to win their home series against India. India won the first Test in Johannesburg by 123 runs, but South Africa avoided what would have been an unprecedented home loss to a team from the Asian sub-continent by winning by 174 runs in Durban and five wickets in Cape Town.
All-rounder Shaun Pollock, whose Test career seemed in decline when he conceded 112 runs and took just one wicket in 35 overs in the second Test against Sri Lanka in August, shone against India with 187 runs at an average of 37.40 and 13 wickets at 16.00.
''Shaun has been awesome, he's realised the role we need him to play for us and he's doing so wonderfully well,'' Arthur said.
Arthur was also satisfied with the form of captain and opening batsman Graeme Smith, who emerged from a slump to score 227 runs at 37.83 against India. Smith passed 50 in each of his last three innings in the series.
''We look a different team when Graeme leads from the front as he did in the last two Tests against India,'' Arthur said.
South Africa retained the squad that played against India for all three Tests against Pakistan.
Squads: South Africa: Graeme Smith (captain), Paul Adams, Hashim Amla, Mark Boucher, AB de Villiers, Herschelle Gibbs, Andrew Hall, Paul Harris, Jacques Kallis, Morne Morkel, Andre Nel, Makhaya Ntini, Shaun Pollock, Ashwell Prince, Jacques Rudolph, Dale Steyn.
Pakistan: Inzamam-ul-Haq (captain), Younis Khan, Asim Kamal, Yasir Hameed, Danish Kaneria, Faisal Iqbal, Imran Farhat, Kamran Akmal, Mohammad Asif, Mohammad Hafeez, Mohammad Sami, Mohammad Yousuf, Naved-ul-Hasan, Shahid Nazir, Shoaib Akhtar, Umar Gul, Zulqarnain Haider.