In my lifetime, yes.
In 1978, a Mizzou team coming off a four-win season beat No. 5 Notre Dame on the road in the season opener. (I was two weeks old at kickoff.) That Notre Dame team finished 9-3 and No. 15 in the nation. Would beating the No. 5 Irish in South Bend - also in a head coach's debut game - go down as more surprising than beating No. 2 Alabama at home? I could hear arguments for both sides.
The 1975 season opened with a win over No. 2 Alabama in Birmingham. That Mizzou team was coming off a 7-4 season that beat a couple ranked teams.
To break down the history more, using the AP rankings, Mizzou is ...
0-15 all-time vs. No. 1 teams
5-16 vs. No. 2 teams ... with the wins coming against No. 2 Kansas in 2007 (not a huge surprise considering MU was No. 3); No. 2 Nebraska in 1973; No. 2 Alabama in 1975; No. 2 Ohio State in 1976 and No. 2 Nebraska in 1978.
Those 1970s teams were all some decent Al Onoforio-built teams that always posted winning records and played some brutal nonconference records ... so I'm not sure I'd count those wins as bigger surprises over a hypothetical win over Bama on Saturday.