Lanning stepped away following the Commonwealth Games in August for personal reasons, missing the WBBL and the five T20Is in India.
"Meg brings so much to the side both on and off the field, and it's pleasing to welcome her back at such an important time with the T20 World Cup just over a month away," national selector Shawn Flegler said "While we welcome Meg back, Alyssa won't have recovered from her calf injury in time, so that presents an opportunity for Beth to take the gloves in her absence.
Australia will have a new-look opening pair with Healy and the retired Rachael Haynes absent from the side that played the ODI World Cup final against England in April.
The three ODIs against Pakistan will take place on January 16, 18 and 21 with the first two matches at Allan Border Field in Brisbane and the last at North Sydney Oval. They are followed by three T20Is on January 24, 26 and 29 before the teams head to South Africa for the World Cup.
Australia squad for Pakistan ODIs Meg Lanning (capt), Tahlia McGrath, Darcie Brown, Nicola Carey, Ashleigh Gardner, Kim Garth, Jess Jonassen (subject to fitness), Alana King, Phoebe Litchfield, Beth Mooney, Ellyse Perry, Megan Schutt, Annabel Sutherland