The top-seeded Dane cruised early but was made to work hard to close out the match in 103 minutes on a balmy evening at Rod Laver Arena.
"My confidence is high, my fitness is good, I feel like my play is improving," Wozniacki beamed in a courtside interview.
"I thought I played a great set and a half and then she started playing very well and got me back on my toes for a bit.
"I'm so happy to be through and even though I know some of the crowd wanted a long match, I hope you'll still support me."
Up a set and coasting at 4-1 in the second, Wozniacki's victory charge was stalled when Jankovic broke back twice to level at 5-5.
But Wozniacki steadied by breaking the Serb again and sealed the match when Jankovic, who notched 50 unforced errors, sprayed a shot long.
The victory allowed Wozniacki to hold onto her top ranking for at least another few days. A number of contenders remain with a chance of swiping it should results go their way in the tournament.
Wozniacki, bidding for her maiden grand slam title, has not dropped a set at Melbourne Park, but faces a far greater test against Kim Clijsters in the quarter-finals.
The four-times grand slam champion Clijsters beat Wozniacki on both their previous meetings, the final of the 2009 US Open and the final of the 2010 Tour Championships.
On Sunday, Clijsters saved four match points as she dug deep to beat China’s Li Na in her fourth round match .
The defending champion, who rolled her ankle midway through the first set and needed medical treatment, came back from 6-2 down in a second set tiebreak to defeat a shellshocked Li 4-6, 7-6, 6-4.
It was a magnificent turnaround from the Belgian, who looked down and out as she hobbled to her chair at 3-3 in the first set after hurting her ankle during a baseline rally.
The much-anticipated rematch of last year’s final had threatened to turn into a huge anti-climax as Clijsters struggled to continue after the fall.
But her sheer determination enthralled the big crowd in the Rod Laver Arena, who swung their support behind the 28 year old, making her last tournament appearance in Australia before retiring at the end of 2012.
“A couple of times it went through my mind (to retire), but I didn’t want to quit at my last time at the Australian Open,” she said.
Earlier in the women's draw, Victoria Azarenka whipped through her match against Iveta Benesova in quick fashion. The Belarussian, seeded third in the draw, took 77 minutes to dismantle her unseeded Czech opponent 6-2, 6-2 to set up a clash against Agnieszka Radwanska, who was also a comfortable winner in the fourth round.
The Polish eighth seed lost only two games as she won 6-1, 6-1 against Julia Goerges, the German 22nd seed.
On the men's side, Roger Federer reached his eighth consecutive Australian Open quarter-final in clinical fashion with a straight sets win over Bernard Tomic.
The Australian teenager, who had idolised Federer as a child, had put the third seed under early pressure, but he could not maintain his play as the 16-time grand slam winner cruised through 6-4, 6-4, 6-2 to set up a last eight encounter with Juan Martin del Potro.
Federer, who has won four times in Melbourne, remains on target for a semi-final with Rafael Nadal.
The world No 2 got the better of Spanish compatriot Feliciano Lopez 6-4, 6-4, 6-2 in their fourth round encounter.
Nadal, coming off three dominant victories, encountered much stiffer resistance from his Davis Cup teammate, a fellow left-hander whose chipping and charging to the net had the Mallorcan repeatedly on the back-foot at the Rod Laver Arena.
The Spaniard came to Melbourne Park under an injury cloud and had his left foot strapped by a physiotherapist early in the first set but moved nimbly enough to wear 30-year-old Lopez in the heat and seal the match in less than two and a half hours.
He was forced to work hard in the first two sets, buthe cruised the final set as he broke Lopez twice to ensure the 2009 champion triumphed in style to advance to his sixth consecutive quarter-final at Melbourne Park, where he will face either Czech seventh seed Tomas Berdych.