The 32-year-old initially trailed defending champion Mads Østberg on Friday morning, but moved into top spot when the Citroën C3 Rally2 driver picked up a puncture and dropped over half a minute.
Østberg fought back in admirable style the following day and at one point cut Mikkelsen’s advantage down to 11.3sec. But disaster struck yet again when he suffered more tyre damage in the Peipsiääre speed test on Saturday.
Mikkelsen started Sunday with a 25.9sec buffer, but was almost caught unawares when Østberg pulled back 7.3sec in the opening speed test.
A burst brake pipe for Østberg enabled the Fabia star to settle down after that, and a calculated drive helped him stay ahead to win by 16.7sec. He now tops the championship standings by 11 points.
"First of all, a big thank you to Toksport and Škoda for providing the car. It's been absolutely perfect all weekend,” beamed Mikkelsen, who last stood on top of the podium in January at Rallye Monte-Carlo.
"We came into this rally really well-prepared, so I am very happy to give the team the result they deserve. It couldn't be better,” he added.
Marco Bulacia was just 11.9sec behind Østberg in another Škoda. The Bolivian claimed a host of stage wins over the weekend and enjoyed a tight tussle with Adrien Fourmaux.
Fourmaux swapped positions with Bulacia multiple times, but an excursion into a field on the penultimate stage was his undoing. The Frenchman eventually trailed his rival by 27.5sec at the finish.
Tom Kristensson enjoyed his first untroubled outing of the season to end 4min 04.3sec back from his Fiesta team-mate, whilst Estonian youngster Georg Linnamäe rounded out the standings another 2min 08.0sec behind in a Volkswagen Polo GTI R5.
Estonia’s high-speed tracks left no margin for error, with a number of high-profile drivers making early exits.
Oliver Solberg was the first to go out in SS4 with engine damage on his Hyundai i20 R5 sustained by a heavy landing. Reigning WRC3 champion Jari Huttunen rolled his similar car in the same stage.
Sean Johnston barrel rolled his C3 on Friday evening, whilst Polo star Nikolay Gryazin was denied a podium when his rally ended upside down at Vastsemõisa.