The signing at NATO headquarters follows a deal with Turkey at last week's NATO summit in Madrid, where Ankara lifted its veto on the Nordic membership bids following assurances that both countries would do more to fight terrorism.
"This is truly an historic moment," NATO Secretary-General Jens Stoltenberg said alongside the foreign ministers of the two countries adding that now that with 32 nations around the table, the alliance will be even stronger.
The protocol means Helsinki and Stockholm can participate in NATO meetings and have greater access to intelligence but will not be protected by the NATO defence clause - that an attack on one ally is an attack against all - until ratification. That is likely to take up to a year.