Hingis' first 35 weeks at No.1 in doubles came in six stints, from June 8 to August 2, 1998 (8 weeks), August 17 to October 25, 1998 (10 weeks), November 2 to 22, 1998 (3 weeks), June 7 to July 4, 1999 (4 weeks), August 2 to 22, 1999 (3 weeks) and January 31 to March 19, 2000 (7 weeks).
She will now begin her 36th career week at the top, while Mirza earns her 41st.
"It's a really nice feeling having that No.1 ahead of your name," Hingis said after the final in Sydney on Friday. "It's definitely something I was aiming for, and with Sania I felt like I had the opportunity to get there. When she became No.1 in Charleston I was just as happy as when I did it myself.
"Being the No.1 team for the last 10 months - we've proven it with two Slams and the WTA Finals in Singapore - we definitely belong there. It was just a question of time to get that No.1 ranking."
"I'm so happy for her that 16 years later she's become No.1 again!" Mirza, who first rose to No.1 last April, commented. "But regardless of what the ranking was, we were the No.1 team in the world.
"I'm so happy that we're together now not just as the No.1 team, but as individuals as well."
The Swiss-Indian duo is on a 30-match winning streak that has brought them seven straight titles at the US Open, Guangzhou, Wuhan, Beijing and WTA Finals in 2015, and Brisbane and Sydney this year.
They'll take that streak - the longest since 1990 - into the Australian Open this fortnight.
Hingis and Mirza are the 11th co-World No.1s in WTA Doubles Rankings history. The full list:
127 weeks - Cara Black & Liezel Huber
82 weeks - Sara Errani & Roberta Vinci
39 weeks - Lisa Raymond & Sam Stosur
20 weeks - Liezel Huber & Lisa Raymond
10 weeks - Kveta Peschke & Katarina Srebotnik
8 weeks - Serena Williams & Venus Williams
7 weeks - Gisela Dulko & Flavia Pennetta
5 weeks - Hsieh Su-Wei & Peng Shuai
3 weeks - Lisa Raymond & Rennae Stubbs
3 weeks - Virginia Ruano Pascual & Paola Suárez
1 week - Martina Hingis & Sania Mirza