The Estonian stopped the clock at 4m31secs on the 3-kilometre second stage of the race, one second ahead of Swede Fredrik Ludvigsson (People4you-Unaas).
Double Tour de France stage winner in 2008 Stefan Schumacher (Christina Watches-Onfone) completed the top three.
The win saw Joeaar assume a four-second lead in the general classification.
The race continues on Friday with a 185km road stage from Tallinn to Tartu and concludes with a road stage of 150km on Saturday.
Stage 2 result:
1 Gert Joeaar (Estonia) 4:31
2 Fredrik Ludvigsson (People4you) +1
3 Stefan Schumacher (Christina Watches) +4
4 Davide Rebellin (CCC) +8
5 Jaroslaw Marycz (CCC) +9
6 Alo Jakin (Estonia) +12
7 Conor McConvey (Synergy) +12
8 Tomasz Kiendys (CCC) +13
9 Martin Mortensen (Concordia) +14
10 Alexander Gingsjo (People4you) +14