The Finn mastered changeable weather conditions to lead the all-Ford Fiesta Rally3 field by 56.0sec after winning all eight superfast gravel stages.
Lauri Joona was Pajari’s nearest challenger despite a puncture in the first stage of the day. He briefly led after Thursday evening’s super special test in Tartu but couldn’t match his compatriot’s pace when the rally got underway in earnest.
“Obviously we have a big lead now, but there is still a long way to go and we can’t take anything for granted,” said a cheery Pajari at the finish.
Motorsport Ireland Rally Academy youngster William Creighton ended 59.6sec behind Joona to complete the leading trio ahead of Mcrae Kimathi, who was the only other driver to finish the leg.
Roope Korhonen’s day ended after just one stage when his Fiesta succumbed to power steering issues and Kaspar Kasari pulled over with mechanical woes on SS7.
• Full coverage from Rally Estonia is available on WRC+ All Live here, including every stage broadcast as it happens as well as key interviews, features and expert analysis from the service park.