Crew members watch as the USNS Comfort arrives at Naval Station Mayport in Jacksonville, Fla., after a six-month deployment. (Bob Mack/Associated Press)

AMERICAN PRESIDENTS rarely veto national defense authorization bills, since they are, well, vital to national security. Since Congress passed the first of these blueprints for Pentagon spending 50-plus years ago, there have been four vetoes — two by Democratic presidents, two by Republicans — according to the House Armed Services Committee. Each time, the president acted because of a disagreement with some policy provision.

As expressed by White House spokesman Josh Earnest, then, President Obama’s threat to veto the fiscal 2016 defense bill that emerged from a House-Senate conference committee and passed the House with bipartisan support on Oct. 1 is a bit unusual: The rationale is procedural.

The $612 billion bill designates $89.2 billion of “overseas contingency” funds — that is, money for warfighting — as regular Department of Defense budget authority (plus nuclear-weapons-related Energy Department programs), so the Pentagon can escape mandatory “sequestration” budget cuts. “That’s an irresponsible way to fund our national defense priorities,” Mr. Earnest declared.

Does the White House have a point? Yes: The overseas contingency budget gimmick is no way to conduct business, doubly objectionable because domestic budget accounts would remain subject to the sequestration caps.

Furthermore, the president months ago made clear his dislike for any bill that might include such a gimmick, so the Republican authors of the bill knew they were sending him veto bait, possibly to score political points by casting Mr. Obama as anti-defense.

In an ideal world, the two parties would be working together on a compromise plan to lift sequestration for both military and domestic programs and pay for the additional spending with offsetting taxes and savings. Those savings would include reforms to entitlements, which are the true cause of our fiscal predicament, not the defense and non-defense discretionary accounts. Come to think of it, in a perfect world, the Obama administration would never have countenanced the sequester’s trade-off between domestic and military spending on the (mistaken) bet that Republicans cared so much about the latter that they would agree to more of the former.

What matters now, however, is that the Pentagon have certainty and predictability in a time of mounting tension in the Middle East and Eastern Europe. The bill’s $612 billion price tag is roughly the total Mr. Obama himself requested. As it happens, the bill also contains important policy changes: major compensation reform that creates retirement savings options for more service members, a ban on torture and $50 million in lethal military aid for Ukraine.

Mr. Obama probably opposes the latter mandate (which the bill would allow his administration to waive), as well as the bill’s continuance of existing constraints on his power to empty and close the prison at Guantanamo. The fact remains: That’s not the main publicly stated reason to veto.

Refusing to sign this bill would make history, but not in a good way. Mr. Obama should let it become law and seek other sources of leverage in pursuing his legitimate goals for domestic sequestration relief.