The beatmaker recently revealed the pair's relationship hit a rocky patch in 2009 after experiencing problems in the studio, prompting Timbaland to skip the 99 Problems hitmaker's age milestone that December.
They have since reconciled, but the producer has now channelled his feelings of remorse over the falling out into a new track, appropriately titled Sorry.
The tune, which features R&B singer/songwriter Keri Hilson, includes the lyrics, "Now we see each other and we don't even speak/That's f**ked up/I missed your 40th and that hurt me so deep/Accept my apology, n**ga please."
Sorry is expected to appear on Timbaland's forthcoming album, Shock Value 3.
Jay Z discussed the dispute during an interview on Britain's BBC Radio 1 earlier this week (begs15Jul13), and suggested a clash of egos was to blame for the incident, which occurred during the making of his release, The Blueprint 3. He said, "When you make an album, you've got to put all ego aside for the sake of the project and he wasn't accepting of that... and that was almost like the last straw... We just went our separate ways... "