The 58-year-old former Australian batsman also believed familiar conditions in the United Arab Emirates (UAE), which has become Pakistan's base as security concerns stop them from hosting matches at home – also give his side edge.
Australia will miss all-rounder Shane Watson through injury and spearhead Brett Lee, who retired last month after being plagued by injuries.
The four-time world champions also slipped to fourth in the on-day rankings earlier this month after a period of three years following their 4-0 loss in England.
The three-match one-day series starts in Sharjah on August 28. The other two matches will be played in Abu Dhabi (August 31) and Sharjah (September 3). The three Twenty20 internationals will be played in Dubai September on 5, 7 and 10.
Whatmore was confident his team will put up a better show.
"Australia have had a retirement or two and an injury so I suppose we can have edge to start with," Whatmore told reporters on team's arrival here on Saturday.
Whatmore, who played seven Test and one limited over international for Australia in late 1970s, warned Australia can come back strongly as well.
"It could be they will try even harder after they lost pretty badly to England but the conditions in UAE are more known to the Pakistan team so from that point of view we hold a bit of an edge," said Whatmore.
Pakistan have been forced to play their home series in UAE since terrorist attacks on the Sri Lankan team suspended all international cricket in the country which prompted foreign teams to refuse tours to the troubled country.
Whatmore believed Pakistan can improve after winning the Asia Cup in March and despite losing both Tests and one-dayers on their tour of Sri Lanka.
"The Asia Cup was good so really it hasn't been as bad as some people may think. I honestly thought we were one ODI victory away from winning the series but otherwise it was a very good tour of Sri Lanka," said Whatmore.
"From positions of strength we managed to snatch defeat and hand the game over," said Whatmore of the 3-1 defeat in the five-match one-day series in Sri Lanka, with one match abandoned due to rain.
"The talent is definitely there, we just need to be a little bit stronger and win the mental battle a bit more and the team will be very competitive and consistent. We're working on those sorts of things."
Whatmore believed Pakistan can do well in the World Twenty20 to be held in Sri Lanka in September-October.
"Pakistan have done impressively well in previous World Twenty20s so the pressure is on for us this time, particularly me. It's a challenge but I've always looked forward to these sorts of challenges."
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PAK TEAM UPPER HAND IN LIMITED OVER MATCHES BECAUSE AUSTRALIA MISS SOME KEY PLAYERS DUE TO INJURIES AND RETIREMENT amazing statement by MR. WHATMORE that mean pak team not capable to face those players who r injured and retired.