Rotherham initially came from two goals down to rescue a 2-2 draw at Wembley, only to then fall behind in a shoot-out as a result of Lee Frecklington's saved effort.
Yet Collin kept out spot-kicks from Mathieu Baudry and Chris Dagnall to lift the New York Stadium outfit into the second tier of English football for the first time since the 2004-05 season.
Russell Slade's men raced into a 2-0 lead against a Rotherham side who were well below their best in the first half.
Moses Odubajo broke the deadlock with a superb strike just after the half-hour mark - hitting a vicious shot that left Collin with no chance.
And Orient were two up before the break when Odubajo latched on to a weak headed clearance from James Tavernier to square for Dean Cox to tap in.
However, former Orient striker Alex Revell inspired a second-half fightback with two goals, the second a stunning effort to send the tie to extra time.
And after coming from behind in normal time, Rotherham successfully did so again in the shoot-out - Collin's save from Dagnall sending fans from South Yorkshire into raptures.
A crowd of 43,401 did not have to wait long for a moment of controversy as Revell went down under a challenge from Nathan Clarke inside the area.
Referee David Coote waved the protests away as Rotherham continued to dominate the early exchanges.
However, Evans' men were dealt two blows before the break as Odubajo's fierce hit put Orient on top before Cox added a second to put his side in a comfortable position.
If Slade's side thought they could coast to victory from there, Rotherham had other ideas, going close with a Ben Pringle free-kick shortly after the interval.
Revell showed his poaching ability to pull one back 10 minutes into the second half with a close-range prod before delivering a goal to outshine Odubajo's earlier effort.
Following an aerial challenge from a long ball, Revell took control and hit a half-volley from well outside the area to restore parity on the hour.
Jones was forced into a reaction save in the first additional period when Scott Cuthbert carelessly headed in the direction of his own goal, but that was as close to either side came to preventing penalties, which eventually went the way of Steve Evans' men.
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