The Spaniard used all his experience to ride a faultless final lap as the Gresini Moriwaki rider came under severe pressure from Qatar winner Tomizawa and Swiss rider Thomas Luthi.
It was a sweet victory for Elias who had been forced to move to the Moto2 class having been bombed out of MotoGP at the end of 2009.
And his victory in the first European Moto2 clash could not have come in more dramatic circumstances after Elias had crashed in the first running of the race.
Tomizawa collided with Simone Corsi at the Curva Dry Sack on lap two and a trail of oil from his Technomag-CIP machine took down eight other riders, including home favourite Elias.
The race was red flagged and cut from the scheduled 26-laps to 17 and the shortened tussle turned out to be a classic encounter.
Elias and Tomizawa figured prominently throughout as a series of close overtakes thrilled a bumper Jerez crowd.
The leading bunch also featured Tech 3 rider Yuki Takahashi, American sensation Kenny Noyes and Corsi.
A shock looked on the cards at one stage when Noyes brilliantly fought his way to the front on lap five with a double swoop by Elias and Tomizawa at the Curva Dry Sack on lap five.
Tomizawa then reclaimed the lead on lap eight, but unlike in Qatar he was unable to make a decision break from the field. A huge rear tyre slide exiting the final corner on the same lap dropped him back to fifth.
But with five laps to go he was back at the front and looking favourite to maintain his 100 per cent record.
But he couldn’t make a clean break with Luthi mounting a superb attack in second. And as the two continually exchanged the lead, it gave the chasing pack chance to get back into contention.
Elias timed his attack to perfection and took second from Tomizawa on the penultimate lap. And he executed a brilliant pass on Luthi at the second corner on the final lap to send the home fans wild.
Elias then defended superbly, particularly at the final corner, to claim his 11th Grand Prix victory and move into second place in the championship.
The 27-year-old, who had finished fourth in the series opener last month, said: “It is unbelievable. Coming to Moto2 I took some risk and before the championship started I had an injury. But everything is going well and to win this race is incredible.”
Tomizawa was second just 0.190s further back with just 1.496s splitting the top six as the Japanese rider had an eventful weekend.
He’d crashed after claiming pole position yesterday and then caused the multi-rider pile-up today.
He said: “I really enjoyed that. The first race wasn’t so good when I crashed at the end of the back straight and the oil I dropped saw many riders crash. I am really sorry about that but we did a great job to get the bike ready and second is a really good result. We are leading the championship and that is a good feeling.”
Luthi deservedly held on for third despite a fierce attack from Japanese rider Takahashi, who missed the podium by just 0.297s.
Luthi said: “It was a really tough race and some of the overtaking was really on the edge. I could make some passes and when I found my pace I thought I could go at a higher level, but it was impossible to pull away.”
Corsi was fifth and Sergio Gadea in sixth with a seventh place scant reward for an eye-catching ride from Noyes.
British rider Scott Redding had an exciting race-long scrap with former Kawasaki MotoGP rider Anthony West.
The Marc VDS Racing rider had to settle for 16th having missed out on his first points-scoring finish by just 0.133s.
1 Toni ELIAS SPA Gresini Racing Moto2 Moriwaki 29’58.726
2 Shoya TOMIZAWA JPN Technomag-CIP Suter +0.190
3 Thomas LUTHI SWI Interwetten Moriwaki Moto2 Moriwaki +0.261
4 Yuki TAKAHASHI JPN Tech 3 Racing Tech 3 +0.558
5 Simone CORSI ITA JIR Moto2 Motobi +1.449
6 Sergio GADEA SPA Tenerife 40 Pons Pons Kalex +1.496
7 Kenny NOYES USA Jack & Jones by A.Banderas Promoharris +2.215
8 Julian SIMON SPA Mapfre Aspar Team RSV +2.576
9 Gabor TALMACSI HUN Fimmco Speed Up Speed Up +3.825
10 Yonny HERNANDEZ COL Blusens-STX BQR-Moto2 +6.691
11 Jules CLUZEL FRA Forward Racing Suter +8.123
12 Roberto ROLFO ITA Italtrans S.T.R. Suter +11.965
13 Dominique AEGERTER SWI Technomag-CIP Suter +12.190
14 Stefan BRADL GER Viessmann Kiefer Racing Suter +12.295
15 Anthony WEST AUS MZ Racing Team MZ-RE Honda +12.545
16 Scott REDDING GBR Marc VDS Racing Team Suter +12.678
17 Ratthapark WILAIROT THA Thai Honda PTT Singha SAG Bimota +13.548
18 Claudio CORTI ITA Forward Racing Suter +15.642
19 Axel PONS SPA Tenerife 40 Pons Pons Kalex +16.740
20 Raffaele DE ROSA ITA Tech 3 Racing Tech 3 +19.368
21 Fonsi NIETO SPA Holiday Gym G22 Moriwaki +20.956
22 Mike DI MEGLIO FRA Mapfre Aspar Team RSV +21.129
23 Vladimir IVANOV UKR Gresini Racing Moto2 Moriwaki +31.224
24 Robertino PIETRI VEN Italtrans S.T.R. Suter +31.275
25 Alex DEBON SPA Aeroport de Castello – Ajo FTR +33.283
26 Lukas PESEK CZE Matteoni CP Racing Moriwaki +34.090
27 Bernat MARTINEZ SPA Maquinza-SAG Team Bimota +38.705
28 Karel ABRAHAM CZE Cardion AB Motoracing RSV +39.384
29 Arne TODE GER Racing Team Germany Suter +43.839
30 Amadeo LLADOS SPA Llados Racing Team AJR +46.896
31 Valentin DEBISE FRA WTR San Marino Team ADV +47.080
32 Alex BALDOLINI ITA Caretta Technology Race Dept I.C.P. +47.216
33 Yannick GUERRA SPA Holiday Gym G22 Moriwaki +47.777
34 Mashel AL NAIMI QAT Blusens-STX BQR-Moto2 +56.595