Morrisons beat a rival offer from EG Group, promising to pay off McColl's £170m debts and take on its 1,160 shops and pension schemes, with 2,000 members.
McColl's was put into administration by PwC on Monday, raising concerns for the staff at stores in Skegness, Chapel St Leonards, Ingoldmells, Boston, Woodhall Spa, Louth and Market Rasen.
On Friday morning supermarket giant Morrisons proposed a last-minute rescue deal for McColl's, which was running out of cash and on the brink of collapse, to save as many jobs as possible..
However later that day, McColl’s confirmed it had gone bust and was appointing administrators.
Rob Lewis, joint administrator and partner at PwC, said the deal provided "much needed certainty to McColl's 16,000 staff after a period of understandable concern".
In a statement, Morrisons' chief executive, David Potts, said: "Although we are disappointed that the business was put into administration, we believe this is a good outcome for McColl's and all its stakeholders.
"This transaction offers stability and continuity for the McColl's business and, in particular, a better outcome for its colleagues and pensioners."
McColl’s traces its roots back to 1901 when a Scottish footballer, Robert Smyth McColl, opened the first RS McColl in Glasgow.2000.
The Group was founded in 1973 starting out as a vending business. In 1994 it purchased Forbouys newsagents and also opened their first food store.