Smith, who had never scored a half-century in one-day games before, managed a sedate 118-ball 101 to guide Australia to a challenging 255-8 before bowlers exposed Pakistan's fragile batting to bowl them out for 162 in 36.3 overs at Sharjah stadium.
Johnson (3-24) combined with off-spinners Glenn Maxwell (2-29) and Nathan Lyon (2-33) bowled with venom and guile to derail Pakistan's chase for Australia's 1-0 lead in the three-match series.
Only Umar Akmal 46 and Sarfraz Ahmed (34) offered some resistance in a poor batting display.
Pakistan lost opener Ahmed Shahzad early for four but make-shift opener Ahmed and Asad Shafiq (13) put on 50 for the second wicket before Pakistan lost three wickets for just four runs.
Lyon had Sarfraz caught behind off a miscued sweep and the next ball had Pakistan skipper Misbah-ul Haq, playing in his 150th one day international, caught at leg-slip by a diving David Warner.
Johnson, who had recovered fully from a rib injury, then had Shafiq off a rising delivery to leave Pakistan reeling at 63-4.
Akmal and Fawad Alam (seven) were all at sea against some vicious spin from Lyon as runs were hard to come by.
As the pressure built up Alam fell to Glenn Maxwell while Shahid Afridi made just five before holing out off Sean Abbott.
All rounder Anwar Ali made just eight before being caught by Brad Haddin off Johnson to cap a good return for the bowler.
Australian captain George Bailey praised Smith and Johnson.

"I think we were 15-20 runs short with the bat but Smith did very well and then there was an outstanding effort with the ball," said Bailey.
"It started to turn a bit, our spinners were effective, good pace from the quicks, backed up well in the field," said Bailey.
Misbah was left ruing another poor batting performance by his team.

"The kind of batting performance we have had, we need to do a lot of things to improve," said Misbah.

"Nobody is getting scores right from the top. That is a big worry for us. We need to come to the next game with a positive attitude."

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