The tourists, replying to Sri Lanka’s first innings score of 416, saw their entire top order wiped out as they struggled to 159 for five by stumps on the second day at the Sinhalese Sports Club.
Ross Taylor was unbeaten on 70 after surviving a close appeal for leg-before by spin king Muttiah Muralitharan when on 30. Brendon McCullum was on five with the tourists still needing 58 more runs to avoid the follow-on.
Samaraweera, who made 159 in the first Test at Galle which Sri Lanka won by 202 runs, hit 143 on way to becoming the second batsman after England captain Andrew Strauss to complete 1,000 runs this year.
New Zealand were reduced to 49 for two when Tim McIntosh was given out leg-before to fast bowler Dammika Prasad for five and Daniel Flynn was caught behind off left-arm seamer Thilan Thushara for 13.
Martin Guptill made a solid 35 when he hooked Thushara to deep square-leg where Muralitharan took an easy catch to make it 63 for three.
Jesse Ryder helped Taylor put on 85 for the fourth wicket, before two quick wickets left the Kiwis reeling.
SCORE BOARD
SRI LANKA (I Innings, O/n: 262/3):
Paranavitana c Taylor b Vettori 19
Dilshan c&b O'Brien 29
Sangakkara c Oram b Vettori 50
M J’wardene c M’Cullum b O'Brien 92
Samaraweera c McCullum b Patel.143
Kapugedera c Vettori b Patel 35
P Jayawardene c O'Brien b Martin..17
Prasad c Taylor b Patel 6
Herath lbw Patel 0
Muralitharan (not out) 17
Thushara c Patel b Vettori 0
Extras: (B-2, LB-5, NB-1) 8
Total (all out; 130.3 overs) 416
Fall of wickets: 1-34, 2-75, 3-115, 4-295, 5-367, 6-389, 7-396, 8-396, 9-415.
Bowling: Martin 24-3-81-1, O'Brien 22-4-73-2, Vettori 40.3-12-104-3, Oram 21-7-56-0, Patel 20-2-78-4, Ryder 3-1-17-0.
New Zealand (I Innings)
McIntosh lbw Prasad 5
Guptill c Muralitharan b Thushara 35
Flynn c P Jayawardene b Thushara .13
Taylor (batting) 70
Ryder c Paranavitana b Herath 23
Patel c M Jayawardene b M’tharan 1
McCullum (batting) 5
Extras (lb-3, W-2, nb-2) 7
Total (for 5 wkts; 47 overs) 159
Fall of wickets: 1-14, 2-49, 3-63, 4-148, 5-149.
Bowling: Dilshan 1-0-6-0, Thushara 9-2-37-2, Prasad 6-0-41-1, Herath 20-8-38-1, Muralitharan 11-1-34-1.