This should give you some hints:
library(grid)
library(ggplot2)
require(gridBase)
par(mfrow = c(2,1))
plot(1:10)
a <- par("mai")
plot.new()
vps <- baseViewports()
pushViewport(vps$figure)
p = qplot(1:10, 1:10) + theme_bw()
g <- ggplotGrob(p)
lw = unit(a[2], "inch") - sum(g$widths[1:3])
g$widths[[2]] <- as.list(lw + g$widths[[2]])
g$widths[[4]] <- as.list(unit(1, "npc") - unit(a[2] + a[4], "inch"))
g$widths[[5]] <- unit(a[4], "inch")
grid.draw(g)
# draw a shaded vertical band to test the alignment
grid.rect(unit(a[2], "inch"), unit(0, "inch"),
unit(1,"npc") - unit(a[2] + a[4], "inch"),
unit(2,"npc"),
gp=gpar(lty=2, fill="red", alpha=0.1), hjust=0, vjust=0)
upViewport()
but, really, why would you not do everything in ggplot2?